Package: a4 Version: 1.55.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 MD5sum: 62328ffcea69c884d330b102c101d1ed NeedsCompilation: no Package: a4Base Version: 1.55.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 3212771821859920375603eac3f30d05 NeedsCompilation: no Package: a4Classif Version: 1.55.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: b7af5109bfba4f239d13ee4ce5e7b36a NeedsCompilation: no Package: a4Core Version: 1.55.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: d2d0ce867df2a7200bb7c0d600fda437 NeedsCompilation: no Package: a4Preproc Version: 1.55.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 8f055b54a4e208d211798f8e4a856e44 NeedsCompilation: no Package: a4Reporting Version: 1.55.0 Imports: methods, xtable Suggests: knitr, rmarkdown License: GPL-3 MD5sum: aa19f45ff368856ba2f39588ce2caa92 NeedsCompilation: no Package: ABarray Version: 1.75.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: b91d31a146a163cdbc7793d6637c94ee NeedsCompilation: no Package: abseqR Version: 1.25.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: cbcbd1e25dac5dcad144c35023f81e0d NeedsCompilation: no Package: ABSSeq Version: 1.61.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: c0631aebbe2996b0cb40d0238b9a9360 NeedsCompilation: no Package: acde Version: 1.37.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: 1fdbcd7b2160ac4e33fe02fbe835e187 NeedsCompilation: no Package: ACE Version: 1.25.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: f824ec9c06fde87add1827987bfb7efa NeedsCompilation: no Package: aCGH Version: 1.85.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, grDevices, graphics, methods, stats, splines, utils License: GPL-2 MD5sum: 2064ffce40ff66812e8e0ddfe976ce13 NeedsCompilation: yes Package: ACME Version: 2.63.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: graphics, stats License: GPL (>= 2) MD5sum: d8506f8f4d510bd085bd48ac6be7f8a6 NeedsCompilation: yes Package: ADaCGH2 Version: 2.47.0 Depends: R (>= 3.2.0), parallel, ff, GLAD Imports: bit, DNAcopy, tilingArray, waveslim, cluster, aCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) MD5sum: 40e18f1bab050760822b058e18fed82f NeedsCompilation: yes Package: ADAM Version: 1.23.0 Depends: R(>= 3.5), stats, utils, methods Imports: Rcpp (>= 0.12.18), GO.db (>= 3.6.0), KEGGREST (>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment (>= 1.10.1) LinkingTo: Rcpp Suggests: testthat, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: dbaeb5e5dc6fde0fc81ca76bd1168a3f NeedsCompilation: yes Package: ADAMgui Version: 1.23.0 Depends: R(>= 3.6), stats, utils, methods, ADAM Imports: GO.db (>= 3.5.0), dplyr (>= 0.7.6), shiny (>= 1.1.0), stringr (>= 1.3.1), stringi (>= 1.2.4), varhandle (>= 2.0.3), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), ggpubr (>= 0.1.8), ggsignif (>= 0.4.0), reshape2 (>= 1.4.3), RColorBrewer (>= 1.1-2), colorRamps (>= 2.3), DT (>= 0.4), data.table (>= 1.11.4), gridExtra (>= 2.3), shinyjs (>= 1.0), knitr, testthat Suggests: markdown, BiocStyle License: GPL (>= 2) MD5sum: 632bb08472109113b822cb93159fc85d NeedsCompilation: no Package: adductomicsR Version: 1.23.0 Depends: R (>= 3.6), adductData, ExperimentHub, AnnotationHub Imports: parallel (>= 3.3.2), data.table (>= 1.10.4), OrgMassSpecR (>= 0.4.6), foreach (>= 1.4.3), mzR (>= 2.14.0), ade4 (>= 1.7.6), rvest (>= 0.3.2), pastecs (>= 1.3.18), reshape2 (>= 1.4.2), pracma (>= 2.0.4), DT (>= 0.2), fpc (>= 2.1.10), doSNOW (>= 1.0.14), fastcluster (>= 1.1.22), RcppEigen (>= 0.3.3.3.0), bootstrap (>= 2017.2), smoother (>= 1.1), dplyr (>= 0.7.5), zoo (>= 1.8), stats (>= 3.5.0), utils (>= 3.5.0), graphics (>= 3.5.0), grDevices (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat License: Artistic-2.0 MD5sum: 99db89d82b1f61e0659c477b5ba9378d NeedsCompilation: no Package: ADImpute Version: 1.17.0 Depends: R (>= 4.0) Imports: checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS, Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 3af750cdbed698a4793c355a1cd64aa9 NeedsCompilation: no Package: adSplit Version: 1.77.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) MD5sum: 46c1eec6c7802ba3e57455ab6d21be48 NeedsCompilation: yes Package: adverSCarial Version: 1.5.0 Depends: R (>= 3.5.0) Imports: gtools, S4Vectors, methods, DelayedArray Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment License: MIT + file LICENSE MD5sum: 6bbbd73bec9bcd776c6ae522a26fa844 NeedsCompilation: no Package: AffiXcan Version: 1.25.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel, crayon Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 44f4b48e88792591ae07616c16f3f4f5 NeedsCompilation: no Package: affxparser Version: 1.79.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 603f98a35bdbf6aa3b8e69b354fa7873 NeedsCompilation: yes Package: affy Version: 1.85.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf License: LGPL (>= 2.0) MD5sum: e2ed8c20e2244d7cab0f55040ef55a0a NeedsCompilation: yes Package: affycomp Version: 1.83.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: e7caeee2cfffbe3e4efb6295d80da4d5 NeedsCompilation: no Package: affyContam Version: 1.65.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata Suggests: hgu95av2cdf License: Artistic-2.0 MD5sum: 5f69f9c8d81c1ae9b131af2a78a3a0c3 NeedsCompilation: no Package: affycoretools Version: 1.79.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 MD5sum: 02f716e8ea8953abdebb5fca14376e95 NeedsCompilation: no Package: affyILM Version: 1.59.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 MD5sum: 899577820895ea4a6f024dd6eb354010 NeedsCompilation: no Package: affyio Version: 1.77.0 Depends: R (>= 2.6.0) Imports: zlibbioc, methods License: LGPL (>= 2) MD5sum: b3f443335570df6f09ae410233059d25 NeedsCompilation: yes Package: affylmGUI Version: 1.81.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi, BiocManager, R2HTML, xtable License: GPL (>= 2) MD5sum: c72be9ad085cb64042a95827f248dae4 NeedsCompilation: no Package: affyPLM Version: 1.83.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS, hgu95av2cdf License: GPL (>= 2) MD5sum: b2965e97b26e34246c5b65bad901aabf NeedsCompilation: yes Package: AffyRNADegradation Version: 1.53.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample, hgu133acdf License: GPL-2 MD5sum: 3599f6abb051706653aff1ce0a2ea6f3 NeedsCompilation: no Package: AGDEX Version: 1.55.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: ba8c9fb26f509d903503a8ef8bd21748 NeedsCompilation: no Package: aggregateBioVar Version: 1.17.0 Depends: R (>= 4.0) Imports: stats, methods, S4Vectors, SummarizedExperiment, SingleCellExperiment, Matrix, tibble, rlang Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis License: GPL-3 MD5sum: a77febdade5c51413201a8ce965d4b8e NeedsCompilation: no Package: agilp Version: 3.39.0 Depends: R (>= 2.14.0) License: GPL-3 MD5sum: 179d01c4b27c42c27006960a75ccc1ed NeedsCompilation: no Package: AgiMicroRna Version: 2.57.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 MD5sum: 20fe00fa29c7140dd6e8091be3df4b06 NeedsCompilation: no Package: AHMassBank Version: 1.7.0 Depends: R (>= 4.2) Imports: AnnotationHubData (>= 1.5.24) Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) License: Artistic-2.0 MD5sum: da7a9bea47b6f2a115478a81358e0bbf NeedsCompilation: no Package: AIMS Version: 1.39.0 Depends: R (>= 2.10), e1071, Biobase Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 2d090c5f9fbd79113cf5af9852d2a97d NeedsCompilation: no Package: airpart Version: 1.15.0 Depends: R (>= 4.1) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, scater, stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue, dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2, ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr License: GPL-2 MD5sum: 34d66622d66550a67adf5f672ab270e4 NeedsCompilation: no Package: alabaster Version: 1.7.0 Depends: alabaster.base Imports: alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sce, alabaster.spatial, alabaster.string, alabaster.vcf, alabaster.bumpy, alabaster.mae Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 3498f82efcc02b1de884a3f017420dfa NeedsCompilation: no Package: alabaster.base Version: 1.7.2 Imports: alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>= 2.47.6), jsonlite, jsonvalidate, Rcpp LinkingTo: Rcpp, assorthead (>= 1.1.2), Rhdf5lib Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix, alabaster.matrix License: MIT + file LICENSE MD5sum: 314e1aea6c001e2f8e46f2552d6c9c2c NeedsCompilation: yes Package: alabaster.bumpy Version: 1.7.0 Depends: BumpyMatrix, alabaster.base Imports: methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite License: MIT + file LICENSE MD5sum: 89b42726caf0473e08a8cd1e210f8f64 NeedsCompilation: no Package: alabaster.files Version: 1.5.0 Depends: alabaster.base, Imports: methods, S4Vectors, BiocGenerics, Rsamtools Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings License: MIT + file LICENSE MD5sum: 8f875b47d8e22a030d50ff7d8b1faea7 NeedsCompilation: no Package: alabaster.mae Version: 1.7.0 Depends: MultiAssayExperiment, alabaster.base Imports: methods, alabaster.se, S4Vectors, jsonlite, rhdf5 Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 5a08ba1123e9fa889e6f35d0a0d993c8 NeedsCompilation: no Package: alabaster.matrix Version: 1.7.2 Depends: alabaster.base Imports: methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.31.8), S4Arrays, SparseArray (>= 1.5.22), rhdf5 (>= 2.47.1), HDF5Array, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, chihaya, BiocSingular, ResidualMatrix License: MIT + file LICENSE MD5sum: 07c65dd47f33111fd5a3cb2efc5a5005 NeedsCompilation: yes Package: alabaster.ranges Version: 1.7.0 Depends: GenomicRanges, alabaster.base Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomeInfoDb, rhdf5 Suggests: testthat, knitr, BiocStyle, jsonlite License: MIT + file LICENSE MD5sum: 9e13e0cdd4626ea45ba1fb995246811b NeedsCompilation: no Package: alabaster.sce Version: 1.7.0 Depends: SingleCellExperiment, alabaster.base Imports: methods, alabaster.se, jsonlite Suggests: knitr, testthat, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: adc1d44686eba44b850ea9886760c9db NeedsCompilation: no Package: alabaster.schemas Version: 1.7.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cf4f1861a12577e03c67957b3681b9fc NeedsCompilation: no Package: alabaster.se Version: 1.7.0 Depends: SummarizedExperiment, alabaster.base Imports: methods, alabaster.ranges, alabaster.matrix, BiocGenerics, S4Vectors, IRanges, GenomicRanges, jsonlite Suggests: rmarkdown, knitr, testthat, BiocStyle License: MIT + file LICENSE MD5sum: e51c4d196f906972636979db7a27b6af NeedsCompilation: no Package: alabaster.spatial Version: 1.7.1 Depends: SpatialExperiment, alabaster.base Imports: methods, utils, grDevices, S4Vectors, alabaster.sce, rhdf5 Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest License: MIT + file LICENSE MD5sum: 8ded4b4af5eaa74f04c88e89f38c41bb NeedsCompilation: no Package: alabaster.string Version: 1.7.0 Depends: Biostrings, alabaster.base Imports: utils, methods, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, testthat License: MIT + file LICENSE MD5sum: dce38c1eecc7fce7496bd9ef69bf499f NeedsCompilation: no Package: alabaster.vcf Version: 1.7.0 Depends: alabaster.base, VariantAnnotation Imports: methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 8eca20e77f60ae14ca434fc28f6b27e7 NeedsCompilation: no Package: ALDEx2 Version: 1.39.0 Depends: methods, stats, zCompositions, lattice, latticeExtra Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick License: GPL (>= 3) MD5sum: 636e554a88f263e444e1cf898ab7f6b7 NeedsCompilation: no Package: alevinQC Version: 1.23.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: ad7008508c74eb537df9ebedfd8774e3 NeedsCompilation: yes Package: AllelicImbalance Version: 1.45.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c9b02c68aba1cbeb935264381056b295 NeedsCompilation: no Package: AlphaBeta Version: 1.21.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 559dd5e89c1c1c25c8dc14e595a98718 NeedsCompilation: no Package: AlphaMissenseR Version: 1.3.0 Depends: R (>= 4.3.0), dplyr Imports: rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, tools, methods, whisker, ggplot2 Suggests: BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, gghalves, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e772d272577cfefc887cc990dfe3c214 NeedsCompilation: no Package: AlpsNMR Version: 4.9.0 Depends: R (>= 4.2) Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.22.0), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel (>= 1.34.0) Suggests: ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) License: MIT + file LICENSE MD5sum: 7c81600d1049b38a8e56b0211adb2045 NeedsCompilation: no Package: altcdfenvs Version: 2.69.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: 0989cc77613dbcdda34a14b05d1dbd7c NeedsCompilation: no Package: AMARETTO Version: 1.23.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: 5eb58c200e109e726ccef47a351fe306 NeedsCompilation: no Package: AMOUNTAIN Version: 1.33.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: 5c60b53754b1a87ba32e4f5154adb4bd NeedsCompilation: yes Package: amplican Version: 1.29.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign, data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: dc731008fd6965c3dbf708433c4a1621 NeedsCompilation: yes Package: Anaquin Version: 2.31.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 0e856eb1dadc4b595d4b250aaa1a1b7b NeedsCompilation: no Package: ANCOMBC Version: 2.9.0 Depends: R (>= 4.3.0) Imports: stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 16aa86319a4bbed42f36f6bbd2070049 NeedsCompilation: no Package: AneuFinder Version: 1.35.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: b44169ab3c45d8d56cd9409a9e8e34ba NeedsCompilation: yes Package: ANF Version: 1.29.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 29bdbbbfac526413f9b46da404d69136 NeedsCompilation: no Package: animalcules Version: 1.23.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: ae926f45efd1b1e112d25ba7e99074a6 NeedsCompilation: no Package: annaffy Version: 1.79.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 96c539beb1dc9ff298ce8e4115cf0e37 NeedsCompilation: no Package: annmap Version: 1.49.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 7fb24c28a01bf519188c5b4b2c573640 NeedsCompilation: no Package: annotate Version: 1.85.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 28437ee87b94a9df3e1ffd22e5cae322 NeedsCompilation: no Package: AnnotationDbi Version: 1.69.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: d5469c79e59a01c6e7fb8b2ad598601f NeedsCompilation: no Package: AnnotationFilter Version: 1.31.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: ca8b2772a588d11e94749ede832c6134 NeedsCompilation: no Package: AnnotationForge Version: 1.49.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: b8150f0487b55cb4cf5885737d22b719 NeedsCompilation: no Package: AnnotationHub Version: 3.15.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 19e24ec71967bcdb4d997d297b840382 NeedsCompilation: yes Package: AnnotationHubData Version: 1.37.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 322757a2bdff450c52d2c710c528986a NeedsCompilation: no Package: annotationTools Version: 1.81.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 4d1d3f136db70fbe1e2ac925ecb2efc7 NeedsCompilation: no Package: annotatr Version: 1.33.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: d41adc950c49f9d23983a7dc0d86c8e6 NeedsCompilation: no Package: anota Version: 1.55.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 19a80e33348fe2d21e93636d83e909e1 NeedsCompilation: no Package: anota2seq Version: 1.29.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: b139eaca9dca1bd1200684276ee51103 NeedsCompilation: no Package: antiProfiles Version: 1.47.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 682ab8563cc1ede647a99c9bbb627000 NeedsCompilation: no Package: AnVIL Version: 1.19.3 Depends: R (>= 3.6), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: 1ea6004ec01262e4413aa1c77a03fa4d NeedsCompilation: no Package: AnVILAz Version: 1.1.0 Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 8bd1154025900ddfdc7b49d26ff3c6aa NeedsCompilation: no Package: AnVILBase Version: 1.1.0 Imports: httr, httr2, dplyr, jsonlite, methods, tibble Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: 9345b146bff0fdecb9dcb0c1ca4af3ea NeedsCompilation: no Package: AnVILBilling Version: 1.17.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 7061c6f5c9868455060600043cfb01dc NeedsCompilation: no Package: AnVILGCP Version: 1.1.1 Imports: AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, httr2, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: befd6ae4d3fac2e1d92d9f7a1dba997d NeedsCompilation: no Package: AnVILPublish Version: 1.17.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 647bc3017ad65d68da1f7d914070113e NeedsCompilation: no Package: AnVILWorkflow Version: 1.7.1 Depends: R (>= 4.4.0), AnVILGCP, AnVILBase, httr Imports: AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 5d3ba276d271fa5e3c5d9a5a9442692d NeedsCompilation: no Package: APAlyzer Version: 1.21.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: 766fc387726984bb62e761772eb56146 NeedsCompilation: no Package: apComplex Version: 2.73.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 968189ac370600e04608e3128e110923 NeedsCompilation: no Package: apeglm Version: 1.29.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: bfadc0ed7ad9917e3b012df2ba06bb31 NeedsCompilation: yes Package: APL Version: 1.11.2 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: e3d117025e223f053b527febdfa3d508 NeedsCompilation: no Package: appreci8R Version: 1.25.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db, utils License: LGPL-3 MD5sum: b134a7e941b76e387e22d21beaaf56ce NeedsCompilation: no Package: aroma.light Version: 3.37.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 5b69addf90fa7b82878c0aa94cf00532 NeedsCompilation: no Package: ArrayExpress Version: 1.67.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 MD5sum: 8856aeb5a97653cc4a442ef6f3801fcb NeedsCompilation: no Package: arrayMvout Version: 1.65.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 876c688ac8b6e581baef58b25b8b3453 NeedsCompilation: no Package: arrayQuality Version: 1.85.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 6bce6f31b56b8c436237b9aee286ea92 NeedsCompilation: no Package: arrayQualityMetrics Version: 3.63.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 384ed988d0ed3372cdb59bfa5f3b3d70 NeedsCompilation: no Package: ARRmNormalization Version: 1.47.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 98f1a1b6dd113b1cbb1ca42b316334e6 NeedsCompilation: no Package: artMS Version: 1.25.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 17efac8bcded7804837f19c96fe3262c NeedsCompilation: no Package: ASAFE Version: 1.33.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 78adca6885dd4645bd03fc5276c379b3 NeedsCompilation: no Package: ASEB Version: 1.51.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 07aef7e57dfe97cfabf7ac0f3cde18d2 NeedsCompilation: yes Package: ASGSCA Version: 1.41.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: a184d8d96778d7a748f28db22e7da39c NeedsCompilation: no Package: ASICS Version: 2.23.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: 5fe9b743a1dc45048f6aa15074829dd6 NeedsCompilation: no Package: ASpli Version: 2.17.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: 157f0527f269762c874416e83220e86e NeedsCompilation: no Package: AssessORF Version: 1.25.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: 039e462f05d0e7a327fb116bab8207f4 NeedsCompilation: no Package: ASSET Version: 2.25.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 124b4fd01505ebdb16c9ac72a63bf7d8 NeedsCompilation: no Package: ASSIGN Version: 1.43.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ffef0fd0ccdeced68898a695c76e60b0 NeedsCompilation: no Package: assorthead Version: 1.1.4 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cf1901b4d790d563c1dc909ca05370bb NeedsCompilation: no Package: ASURAT Version: 1.11.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 8dbf2451372b8c87c754210855ce6a16 NeedsCompilation: yes Package: ATACseqQC Version: 1.31.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 9c1a54d63fb3e172f3cc7bebbe403f6e NeedsCompilation: no Package: ATACseqTFEA Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: f4c623a8be30975a924fb0966d54d7aa NeedsCompilation: no Package: atena Version: 1.13.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: 1fab4bf559cf56d156964892c504500a NeedsCompilation: no Package: atSNP Version: 1.23.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 6656fa02ff06add1a723bde24144336e NeedsCompilation: yes Package: attract Version: 1.59.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 264fdbcea205735ab3a1381afdb3454e NeedsCompilation: no Package: AUCell Version: 1.29.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 103051bd69a9ca5c471c19bd390de490 NeedsCompilation: no Package: autonomics Version: 1.15.10 Depends: R (>= 4.0) Imports: abind, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, patchwork, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 75e856e4dd297e2769249514e5888fdc NeedsCompilation: no Package: AWFisher Version: 1.21.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 0602334dbc6589da5167f454a8b0c648 NeedsCompilation: yes Package: awst Version: 1.15.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 0d6a16c233e2cf9864f31c3541db9641 NeedsCompilation: no Package: BaalChIP Version: 1.33.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b6079c678f35e00f366764f6d8bea167 NeedsCompilation: no Package: bacon Version: 1.35.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 06f4df3cdb3d32f4e4208ac8e422e6cc NeedsCompilation: yes Package: BADER Version: 1.45.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 920547d8385d607bd44ab521b2194a7d NeedsCompilation: yes Package: BadRegionFinder Version: 1.35.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 1336ea45fb9b6fc1f2e7d4e93ff78e90 NeedsCompilation: no Package: BAGS Version: 2.47.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 0518901a34fd1ce02204c70610a24643 NeedsCompilation: yes Package: ballgown Version: 2.39.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: 5a7b7ddfe9719786ea7426b55d35004a NeedsCompilation: no Package: bambu Version: 3.9.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 704a50ba91399f59332f7a60002cf36b NeedsCompilation: yes Package: bamsignals Version: 1.39.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 21b24310dd7ac2802c46f29229a635e1 NeedsCompilation: yes Package: BANDITS Version: 1.23.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 9d982541e644148f58eed67401af3168 NeedsCompilation: yes Package: bandle Version: 1.11.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 5440ced877a2fce71e7e80523fc6be15 NeedsCompilation: yes Package: Banksy Version: 1.3.0 Depends: R (>= 4.4.0) Imports: aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: 70aad5f8c35fa430d4207cca69e4a028 NeedsCompilation: no Package: banocc Version: 1.31.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 38a45c0d9b5eb383145f94a89f33cf7b NeedsCompilation: no Package: barcodetrackR Version: 1.15.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 30804183e779bef73e3f0ffa6dc834c3 NeedsCompilation: no Package: basecallQC Version: 1.31.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 9f94546a5874cd0dd73ea7e27e4a05e8 NeedsCompilation: no Package: BaseSpaceR Version: 1.51.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 60a85ce955f7f16cd0ba3877739ec5f1 NeedsCompilation: no Package: Basic4Cseq Version: 1.43.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 02b070751ffdef4ac7ff5ab2275ce5ac NeedsCompilation: no Package: BASiCS Version: 2.19.0 Depends: R (>= 4.2), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: 47d03ece2932df001918e7b196663328 NeedsCompilation: yes Package: BASiCStan Version: 1.9.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: 4bb22cfad535d8e851a31be1229b75d5 NeedsCompilation: yes Package: BasicSTARRseq Version: 1.35.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: fd028ff1976d44806e2f5baadd9c3df7 NeedsCompilation: no Package: basilisk Version: 1.19.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: c74f04ca170b25eb3090687276e9471b NeedsCompilation: no Package: basilisk.utils Version: 1.19.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 MD5sum: 9b92c90fefe00444b19cb9e14327776e NeedsCompilation: no Package: batchelor Version: 1.23.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: 4459733830062d871a5f380496b0a88f NeedsCompilation: yes Package: BatchQC Version: 2.3.0 Depends: R (>= 4.4.0) Imports: data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse, utils Suggests: BiocManager, BiocStyle, bladderbatch, devtools, knitr, lintr, plotly, rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7945c5c6aa72a5f03070a0a1ff9ecb55 NeedsCompilation: no Package: BayesKnockdown Version: 1.33.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: 2b10851e3e118c3688b7dd4c3dd422d6 NeedsCompilation: no Package: BayesSpace Version: 1.17.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr, assertthat, arrow, mclust, RCurl, DirichletReg, xgboost, utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr, scales, microbenchmark, BiocFileCache, BiocSingular, BiocParallel LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: 88f1b1cbc590dca239a4e62a56c017df NeedsCompilation: yes Package: bayNorm Version: 1.25.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 23021fdb29ca4125b43ef68365859b66 NeedsCompilation: yes Package: baySeq Version: 2.41.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: a96b38865d70d03e6168939f728da2d9 NeedsCompilation: no Package: BBCAnalyzer Version: 1.37.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 9779167737fbabaa62a3f5b0bb2fa146 NeedsCompilation: no Package: BCRANK Version: 1.69.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 11000adaf73797a7e630b4d625555877 NeedsCompilation: yes Package: bcSeq Version: 1.29.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: dcf650b96ba37c187a19acb2243ba4a5 NeedsCompilation: yes Package: beachmat Version: 2.23.1 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 0b5e037fee7f87e0900f0be42be92b8e NeedsCompilation: yes Package: beachmat.hdf5 Version: 1.5.1 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: a841100d53c8f80932640d341fc76dff NeedsCompilation: yes Package: beadarray Version: 2.57.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 02956ab2acc1faa0badbca5bd8551e59 NeedsCompilation: yes Package: BeadDataPackR Version: 1.59.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 5a8b747f2f49e7de530875c8317317a0 NeedsCompilation: yes Package: BEAT Version: 1.45.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 2f497cd941fbe43419b072852d902603 NeedsCompilation: no Package: BEclear Version: 2.23.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: 5849131ee57651736825fcdda68ef89e NeedsCompilation: yes Package: beer Version: 1.11.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 264840163396abbe89cc55d4dc26e671 NeedsCompilation: no Package: BERT Version: 1.3.3 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ac7d88402ecfeef96b497ec5397725fb NeedsCompilation: no Package: betaHMM Version: 1.3.0 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 13293c20fbce750c27f3defbbba0e3e1 NeedsCompilation: no Package: bettr Version: 1.3.0 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 5d351b8e5102f9b105538147bbcf5a6b NeedsCompilation: no Package: BG2 Version: 1.7.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: d06334428c613f24a3a048a96ed80a4a NeedsCompilation: no Package: BgeeCall Version: 1.23.0 Depends: R (>= 3.6) Imports: GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE MD5sum: 8da90e529bd64c17c33576be7dc45561 NeedsCompilation: no Package: BgeeDB Version: 2.33.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 7f1c95bcf8dc4719a6a047de1f46dc3f NeedsCompilation: no Package: BicARE Version: 1.65.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: eac5a310d8a0fc33b9987f2a3dc5dc8d NeedsCompilation: yes Package: BiFET Version: 1.27.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: c3dd5495961c83e465ef09090940abe1 NeedsCompilation: no Package: BiGGR Version: 1.43.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr Imports: hypergraph, limSolve License: file LICENSE MD5sum: eda2ca1b253d1ebdf99aa8220d34cf0f NeedsCompilation: no Package: bigmelon Version: 1.33.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: 34b6cebd14e45318d7eb5b1c8e4e07b0 NeedsCompilation: no Package: BindingSiteFinder Version: 2.5.1 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr License: Artistic-2.0 MD5sum: 33782d14619c64174cf96bc3d551a621 NeedsCompilation: no Package: bioassayR Version: 1.45.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: BiocStyle, RCurl, biomaRt, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown License: Artistic-2.0 MD5sum: 3f731a6c089f39ca23d0e77312b07cc8 NeedsCompilation: no Package: Biobase Version: 2.67.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 MD5sum: bb1f78e974248f618f28dfbc26539935 NeedsCompilation: yes Package: biobroom Version: 1.39.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 718605b97a56dec6715663add12cb227 NeedsCompilation: no Package: biobtreeR Version: 1.19.0 Imports: httr, httpuv, stringi,jsonlite,methods,utils Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown License: MIT + file LICENSE MD5sum: 25b9527aa216a5e828aae6799b75bbde NeedsCompilation: no Package: bioCancer Version: 1.35.0 Depends: R (>= 3.6.0), radiant.data (>= 0.9.1), cBioPortalData, XML(>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble, GO.db Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: 43e9a8e6f696a8f0790a34dbf65373e5 NeedsCompilation: no Package: BioCartaImage Version: 1.5.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, BiocStyle, ragg License: MIT + file LICENSE MD5sum: 2391621ba4351ffa2c100c084b2b60d4 NeedsCompilation: no Package: BiocBaseUtils Version: 1.9.0 Depends: R (>= 4.2.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 MD5sum: dac17bda4b452bb7e95cd3ecb2c90aa3 NeedsCompilation: no Package: BiocCheck Version: 1.43.2 Depends: R (>= 4.4.0) Imports: BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr, cli, codetools, graph, httr2, knitr, methods, rvest, stringdist, tools, utils Suggests: BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest, usethis License: Artistic-2.0 MD5sum: 4f68ad984c7f55994fdc05517956b3ff NeedsCompilation: no Package: BiocFHIR Version: 1.9.0 Depends: R (>= 4.2) Imports: DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle License: Artistic-2.0 MD5sum: b1f1d73fbbd0d77985664635c8b78cf1 NeedsCompilation: no Package: BiocFileCache Version: 2.15.0 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: 2acb42ad120f0ad99b8ddff455e7f958 NeedsCompilation: no Package: BiocGenerics Version: 0.53.3 Depends: R (>= 4.0.0), methods, utils, graphics, stats, generics Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, S4Arrays, SparseArray, DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit License: Artistic-2.0 MD5sum: 3d35210a258114d23c74084c4401b47c NeedsCompilation: no Package: biocGraph Version: 1.69.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: a574b9d9496b25fbe3b7e824762b3cb0 NeedsCompilation: no Package: BiocHail Version: 1.7.1 Depends: R (>= 4.3.0), graphics, stats, utils Imports: reticulate, basilisk, BiocFileCache, methods, dplyr, BiocGenerics Suggests: knitr, testthat, BiocStyle, ggplot2, DT License: Artistic-2.0 MD5sum: e87088a34de49f92f991cd95c85d7b23 NeedsCompilation: no Package: BiocHubsShiny Version: 1.7.1 Depends: R (>= 4.3.0), shiny Imports: AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard, S4Vectors, shinyAce, shinyjs, shinythemes, shinytoastr, utils Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 License: Artistic-2.0 MD5sum: dce9c1f48c667b70bc34fac1af03a29d NeedsCompilation: no Package: BiocIO Version: 1.17.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, S4Vectors, methods, tools Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ad99a0894e5a31d7a0c7c5748ca3033b NeedsCompilation: no Package: BiocNeighbors Version: 2.1.0 Imports: Rcpp, methods LinkingTo: Rcpp, assorthead Suggests: BiocParallel, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2a2efebd8385216f7515ecaddeb83363 NeedsCompilation: yes Package: BioCor Version: 1.31.0 Depends: R (>= 3.4.0) Imports: BiocParallel, GSEABase, Matrix, methods Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat (>= 3.0.0), WGCNA License: MIT + file LICENSE MD5sum: c993714b686a5c2ecca3bf1eb7654573 NeedsCompilation: no Package: BiocParallel Version: 1.41.0 Depends: methods, R (>= 3.5.0) Imports: stats, utils, futile.logger, parallel, snow, codetools LinkingTo: BH, cpp11 Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table Enhances: Rmpi License: GPL-2 | GPL-3 MD5sum: 9242165148fc3b13775ac18becde63bd NeedsCompilation: yes Package: BiocPkgTools Version: 1.25.2 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, magrittr, methods, rlang, stringr, stats, rvest, dplyr, xml2, readr, httr, htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL, graph, rorcid Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE MD5sum: 06f890a7e4dd021a66012b7604a69af8 NeedsCompilation: no Package: biocroxytest Version: 1.3.0 Depends: R (>= 4.4.0) Imports: cli, glue, roxygen2, stringr Suggests: BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 7ffcf9a9655ceec87ad93009348ffbed NeedsCompilation: no Package: BiocSet Version: 1.21.0 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 684c60b9923e24193278df574ae10c8d NeedsCompilation: no Package: BiocSingular Version: 1.23.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>= 2.21.1) LinkingTo: Rcpp, beachmat, assorthead Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 MD5sum: 73c5f4c0bb232ab7d2de94bff775cde3 NeedsCompilation: yes Package: BiocSklearn Version: 1.29.0 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment Imports: basilisk Suggests: testthat, HDF5Array, BiocStyle, rmarkdown, knitr License: Artistic-2.0 MD5sum: 9f3331d740d8444917b8d4068b164d24 NeedsCompilation: no Package: BiocStyle Version: 2.35.0 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 MD5sum: 397df8a5405591881755daa79d907f7c NeedsCompilation: no Package: biocthis Version: 1.17.0 Imports: BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1) Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils License: Artistic-2.0 MD5sum: 490cd416f48c19a4b23b8d720c65e015 NeedsCompilation: no Package: BiocVersion Version: 3.21.1 Depends: R (>= 4.5.0) License: Artistic-2.0 MD5sum: 58ff0a6132b77db8a38aad3668ea3e11 NeedsCompilation: no Package: biocViews Version: 1.75.0 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark, BiocStyle License: Artistic-2.0 MD5sum: 79a4d8013922b825f35d532d8f4be6df NeedsCompilation: no Package: BiocWorkflowTools Version: 1.33.0 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE MD5sum: c33e3dda8d6e76bc6ae282057ccecd70 NeedsCompilation: no Package: biodb Version: 1.15.0 Depends: R (>= 4.1.0) Imports: BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r, jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, stats, stringr, tools, withr, yaml LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 License: AGPL-3 MD5sum: 0bf7bc73882fd9b4126ef77971ac373c NeedsCompilation: yes Package: biodbChebi Version: 1.13.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.1.5) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr License: AGPL-3 MD5sum: 7f9c2e3e15310e90c10fd5579c3e20c2 NeedsCompilation: no Package: biodbHmdb Version: 1.13.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.3.2), Rcpp, zip LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 441674ec510115b14cecd2707f115882 NeedsCompilation: yes Package: biodbNcbi Version: 1.11.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.2), R6, XML, chk Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 8980bc87be701b854c81965cc860bc01 NeedsCompilation: no Package: biodbNci Version: 1.11.0 Depends: R (>= 4.1) Imports: biodb (>= 1.3.1), R6, Rcpp, chk LinkingTo: Rcpp, testthat Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr License: AGPL-3 MD5sum: 32ed12e5d8513dbb30c72d9e3902a66a NeedsCompilation: yes Package: biodbUniprot Version: 1.13.0 Depends: R (>= 4.1.0) Imports: R6, biodb (>= 1.4.2) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr License: AGPL-3 MD5sum: 3315e1a472bd14a76ead171e22cf04cb NeedsCompilation: no Package: bioDist Version: 1.79.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: e822979703d707013640accf415f0a00 NeedsCompilation: no Package: BioGA Version: 1.1.0 Depends: R (>= 4.4) Imports: ggplot2, graphics, Rcpp, SummarizedExperiment, animation, rlang, biocViews, sessioninfo, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 0f6b1f9143073e3cae00d4ed8fc9ca29 NeedsCompilation: yes Package: biomaRt Version: 2.63.0 Depends: methods Imports: utils, AnnotationDbi, progress, stringr, httr2, digest, BiocFileCache, rappdirs, xml2, curl Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2 License: Artistic-2.0 MD5sum: 4e8ac02e5544fdffa47103f5919aa34c NeedsCompilation: no Package: biomformat Version: 1.35.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: a95d2efd7d733cbccc96aec0e17b7aa4 NeedsCompilation: no Package: BioMVCClass Version: 1.75.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: d118422b5114c999e4b0728ec566e4ec NeedsCompilation: no Package: biomvRCNS Version: 1.47.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: eae8b3e80a6262c3b6a80a9707a6fc86 NeedsCompilation: yes Package: BioNAR Version: 1.9.0 Depends: R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp, RSpectra, Rdpack Imports: stringr, viridis, clusterCons, fgsea, grid, methods, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2, ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 MD5sum: 371ef384e732c61fed8664b6e8bbbb5f NeedsCompilation: no Package: BioNERO Version: 1.15.0 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr License: GPL-3 MD5sum: 87e1f16d89087129db755176edd6d2aa NeedsCompilation: no Package: BioNet Version: 1.67.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 24ed1488c9424d4359f29c4c4dd21a40 NeedsCompilation: no Package: BioQC Version: 1.35.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: c5b8fb40c96c3dfce66cf5a3e582c629 NeedsCompilation: yes Package: biosigner Version: 1.35.0 Imports: Biobase, methods, e1071, grDevices, graphics, MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats, SummarizedExperiment, utils Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 45ea92ddcfb689837fd6d9bde14a9e88 NeedsCompilation: no Package: Biostrings Version: 2.75.1 Depends: R (>= 4.0.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), GenomeInfoDb Imports: methods, utils, grDevices, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: graphics, pwalign, BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: bdf0772e32fc7af4d85e4be9352d7b6f NeedsCompilation: yes Package: BioTIP Version: 1.21.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges, MASS, scran Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 MD5sum: 67584ffd07854144fd66d2462f5f2a95 NeedsCompilation: no Package: biotmle Version: 1.31.0 Depends: R (>= 4.0) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE MD5sum: d2556e05683a882534894366b6344a18 NeedsCompilation: no Package: biovizBase Version: 1.55.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: d8873e007c9c6a7066a319acdf723e82 NeedsCompilation: yes Package: BiRewire Version: 3.39.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 0fd2539da644b312a3ba3b5dddb6275e NeedsCompilation: yes Package: biscuiteer Version: 1.21.0 Depends: R (>= 4.1.0), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle License: GPL-3 MD5sum: 1fbd4eaa98633c7ce8008eb447a3e7dc NeedsCompilation: no Package: BiSeq Version: 1.47.0 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: e822404b65d3bc4b042a51b7f8f92b0f NeedsCompilation: no Package: blacksheepr Version: 1.19.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: 9890098d8395b6a9728307a006c6dff1 NeedsCompilation: no Package: blima Version: 1.41.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: f855c2e6d71b12431f2dadd6717b556c NeedsCompilation: yes Package: BLMA Version: 1.31.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 2ac66c3cc15d2f2cc789ac408584de21 NeedsCompilation: no Package: BloodGen3Module Version: 1.15.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 664258ed1f8ec1dd4f826257d04bce9e NeedsCompilation: no Package: bluster Version: 1.17.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp, assorthead Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster License: GPL-3 MD5sum: 76202e3d1ed5b0e0b51b5db7570cd3e3 NeedsCompilation: yes Package: bnbc Version: 1.29.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils, HiCBricks LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: d9537db99ad482734e1d8caf242a61f5 NeedsCompilation: yes Package: bnem Version: 1.15.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: da0e2f4a7c24868dae9b147bf4f83f72 NeedsCompilation: no Package: BOBaFIT Version: 1.11.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: d48a94d844122e83472cc50ccbffe68f NeedsCompilation: no Package: borealis Version: 1.11.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: 4525256e8268c65c9f29050ba3140831 NeedsCompilation: no Package: BPRMeth Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 84c0b179902afccd9acf30d4d52d9b28 NeedsCompilation: yes Package: BRAIN Version: 1.53.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 0972cf7fdcdf11caff0f71640ea4bd2e NeedsCompilation: no Package: branchpointer Version: 1.33.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 68736754ab3004999df0990ba4acb7fa NeedsCompilation: no Package: breakpointR Version: 1.25.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 45d40475f8b3c711590207c96854c974 NeedsCompilation: no Package: brendaDb Version: 1.21.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: c5a5fed736ff4c22dd5990fb1173a7c7 NeedsCompilation: yes Package: BREW3R.r Version: 1.3.0 Imports: GenomicRanges, methods, rlang, S4Vectors, utils Suggests: testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer License: GPL-3 MD5sum: 0984a60c2e7f466025e5ccfc45623f02 NeedsCompilation: no Package: BridgeDbR Version: 2.17.1 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: fde2bac38f709d8274f6b0e962d10a7e NeedsCompilation: no Package: broadSeq Version: 1.1.0 Depends: dplyr, ggpubr, SummarizedExperiment Imports: BiocStyle, DELocal, EBSeq (>= 1.38.0), DESeq2 (>= 1.38.2), NOISeq, forcats (>= 1.0.0), genefilter, ggplot2, ggplotify, plyr, clusterProfiler (>= 4.8.2), pheatmap, sechm (>= 1.6.0), stringr, purrr (>= 0.3.5), edgeR (>= 3.40.1) Suggests: knitr, limma (>= 3.54.0), rmarkdown, stats (>= 4.2.2), samr License: MIT + file LICENSE MD5sum: b5f1ff8623c91377dccf3d99847ee9c7 NeedsCompilation: no Package: BrowserViz Version: 2.29.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 8dbfedeed23f178c6468fb2a622f46fa NeedsCompilation: no Package: BSgenome Version: 1.75.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), BiocIO, rtracklayer Imports: utils, stats, matrixStats, XVector, Rsamtools Suggests: BiocManager, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge License: Artistic-2.0 MD5sum: 279fa9c8685d5609cf3a56b9166a6554 NeedsCompilation: no Package: BSgenomeForge Version: 1.7.0 Depends: R (>= 4.3.0), methods, BiocGenerics, IRanges, GenomeInfoDb (>= 1.33.17), Biostrings, BSgenome Imports: utils, stats, Biobase, S4Vectors, GenomicRanges, BiocIO, rtracklayer Suggests: GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 License: Artistic-2.0 MD5sum: e93b7e14d76e1849508c026992096e89 NeedsCompilation: no Package: bsseq Version: 1.43.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, parallel, tools, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools License: Artistic-2.0 MD5sum: eae5e11b9d81e44d03fb719ac8f28b42 NeedsCompilation: yes Package: BubbleTree Version: 2.37.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 297d6761d3befaafb608706b95ba8f9e NeedsCompilation: no Package: BufferedMatrix Version: 1.71.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: 81bd4d1beb50d968eede7df045f548c5 NeedsCompilation: yes Package: BufferedMatrixMethods Version: 1.71.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: a356159645aa62e473e5be4eeed684ff NeedsCompilation: yes Package: bugsigdbr Version: 1.13.0 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: f1c7ebf9dff72656fb538c7191c28b6e NeedsCompilation: no Package: BUMHMM Version: 1.31.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 89a9a3c50b1209fa3b04d9f30af0cd22 NeedsCompilation: no Package: bumphunter Version: 1.49.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 2b7e58aba276896434435ee20d929eac NeedsCompilation: no Package: BumpyMatrix Version: 1.15.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: c67043ff427cc53eecf4388465a7539b NeedsCompilation: no Package: BUS Version: 1.63.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 4dbbe1d0a01fcaa01290b052bbea0c97 NeedsCompilation: yes Package: BUScorrect Version: 1.25.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: c4e6e6b1243c792c85ba6800cc5fc57c NeedsCompilation: yes Package: BUSpaRse Version: 1.21.0 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, txdbmaker, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: b1f4571234413c981dd2e10c8200cc70 NeedsCompilation: yes Package: BUSseq Version: 1.13.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: ac230a447b9df708273967590baad515 NeedsCompilation: yes Package: CaDrA Version: 1.5.0 Depends: R (>= 4.4.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: ece8ce52575aeaa3f6ade6490b47de32 NeedsCompilation: yes Package: CAEN Version: 1.15.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: 1efc21f5728b88ef1b31a4c684b1394b NeedsCompilation: no Package: CAFE Version: 1.43.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: cc62358039c41de986c0bd63b6e20404 NeedsCompilation: no Package: CAGEfightR Version: 1.27.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 970a7e0c9e0820b2285805b26083eae6 NeedsCompilation: no Package: cageminer Version: 1.13.0 Depends: R (>= 4.1) Imports: ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 42fd5350c01354a81a2439cc1f528f87 NeedsCompilation: no Package: CAGEr Version: 2.13.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, rlang, Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 023128492841632e777bbb7223cfc272 NeedsCompilation: no Package: calm Version: 1.21.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: f087b619ff82097bdf60afb609ed6efe NeedsCompilation: no Package: CAMERA Version: 1.63.0 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics, multtest Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: e65dc944e1fd00a1801fcf24a5ea96c3 NeedsCompilation: yes Package: CaMutQC Version: 1.3.0 Depends: R (>= 4.0.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 31bc0a2ace40b7f805c9e91516306752 NeedsCompilation: no Package: canceR Version: 1.41.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 7194bb476457a01b444c7ba9370b6733 NeedsCompilation: no Package: cancerclass Version: 1.51.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 4bc0b2a19abfa70beb2c5802db1e0abd NeedsCompilation: yes Package: cardelino Version: 1.9.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 8185c2a2a54c7337598cb46df5af2560 NeedsCompilation: yes Package: Cardinal Version: 3.9.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: b81231f3abf7fed1186511c77fb6e0af NeedsCompilation: no Package: CardinalIO Version: 1.5.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 24d27af8711f95c79bb491a4d0c1c463 NeedsCompilation: yes Package: CARNIVAL Version: 2.17.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 2ec647013758017a8d0417676a8cf481 NeedsCompilation: no Package: casper Version: 2.41.0 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: ea9ea0ebb467878ab14d59cf70152ba4 NeedsCompilation: yes Package: CATALYST Version: 1.31.0 Depends: R (>= 4.4), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: c0b6ceeb100fceff5d7528a65b573c1f NeedsCompilation: no Package: Category Version: 2.73.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 0c16729015a364a2bc797c3fded93722 NeedsCompilation: no Package: categoryCompare Version: 1.51.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: 72c8c2eddca7f53c761eef32aa62692a NeedsCompilation: no Package: CatsCradle Version: 1.1.0 Depends: R (>= 4.4.0) Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr Suggests: fossil, interp, knitr, BiocStyle, tictoc License: MIT + file LICENSE MD5sum: 664491efc8de03a84822e90cf43b45a8 NeedsCompilation: no Package: CausalR Version: 1.39.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: bf244fa8787cc9dececec2abb351c8ba NeedsCompilation: no Package: cbaf Version: 1.29.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1d5fd634d496cc654aed208ec315f350 NeedsCompilation: no Package: cBioPortalData Version: 2.19.1 Depends: R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: 78ccfb2c1c6b31bc454df282c46a86c2 NeedsCompilation: no Package: CBNplot Version: 1.7.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 32889a2dd375ebbefbbb69323024fa5e NeedsCompilation: no Package: cbpManager Version: 1.15.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 6580ed7b3e0bfe90a16f4ae66b2e49f4 NeedsCompilation: no Package: ccfindR Version: 1.27.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 976fbc36a6f78b10a00296780d68b2f0 NeedsCompilation: yes Package: ccImpute Version: 1.9.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: e9dbeeb9bab1f5880eba31680b89b879 NeedsCompilation: yes Package: ccmap Version: 1.33.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: 282fad9f0e9ea248e78b7a64c78d4ca1 NeedsCompilation: no Package: CCPlotR Version: 1.5.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c60aa852df6f1e4bec5b2ef92f860da4 NeedsCompilation: no Package: CCPROMISE Version: 1.33.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 5648a2e22e45edc3ecc8dee5d7a94f54 NeedsCompilation: no Package: ccrepe Version: 1.43.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: d0b6bd3c7bc4bde3a9c4283e0e0da0d9 NeedsCompilation: no Package: CDI Version: 1.5.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: 74a2766784769e03adbc1a581b0bbd7a NeedsCompilation: no Package: celaref Version: 1.25.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 694bb2a78f54ff36d76fd76f7ff7c627 NeedsCompilation: no Package: celda Version: 1.21.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 251f04b5857b7945db8e5d6c8b4b6a70 NeedsCompilation: yes Package: CellBarcode Version: 1.13.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, zlibbioc, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: f167713f34d20a9bd6f87a21c991cd6d NeedsCompilation: yes Package: cellbaseR Version: 1.31.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: f815692fd7071cffe16bdd4e672e1a89 NeedsCompilation: no Package: CellBench Version: 1.23.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: f307b90e08b6a67eece0e6acbcf2b3b2 NeedsCompilation: no Package: CelliD Version: 1.15.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: 8f30993883fc40954f998e189f5e31a2 NeedsCompilation: yes Package: cellity Version: 1.35.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: bef43724dd0edf1636ca6ad6f1cea0b6 NeedsCompilation: no Package: CellMapper Version: 1.33.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: fe5dab5461e3585f50d53bbb6470a492 NeedsCompilation: no Package: cellmigRation Version: 1.15.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 871eaa3d8450f20a1901eb12c9a7f6b5 NeedsCompilation: no Package: CellMixS Version: 1.23.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 6afeca36732eaefa9ff7dc97c945651a NeedsCompilation: no Package: CellNOptR Version: 1.53.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: 6b1089bb60cb261cf36c16d4bc5d8f6c NeedsCompilation: yes Package: cellscape Version: 1.31.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: e51470c789844af8f45a1ea0d155a384 NeedsCompilation: no Package: CellScore Version: 1.27.0 Depends: R (>= 4.3.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0), SummarizedExperiment Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 4464713764559ce74fe042e27133ba3a NeedsCompilation: no Package: CellTrails Version: 1.25.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 4779e915b71aef01628b8d5e579ad7d7 NeedsCompilation: no Package: cellxgenedp Version: 1.11.0 Depends: dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 1161a0d753031ead9908340f785b93c5 NeedsCompilation: no Package: CEMiTool Version: 1.31.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 44ee1f61bab5626fc0f0a6983218540f NeedsCompilation: no Package: censcyt Version: 1.15.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: e5461b6d2f9a4598ea9bde932891c747 NeedsCompilation: no Package: Cepo Version: 1.13.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 9d149c1c4b3d3d15fe020c4c6f9f350a NeedsCompilation: no Package: ceRNAnetsim Version: 1.19.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 56b8a4b953f86d03c4cc8abf8b99d37e NeedsCompilation: no Package: CeTF Version: 1.19.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 51c52b25f8d3799f875c97d8490a5eea NeedsCompilation: yes Package: CexoR Version: 1.45.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 00e2267743777706e78422dc6b12ab36 NeedsCompilation: no Package: CFAssay Version: 1.41.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: 2563526d2bc93f18eadda8a99991a572 NeedsCompilation: no Package: cfdnakit Version: 1.5.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: 4c99e84a52eb8c2e6c4fa21882f2d009 NeedsCompilation: no Package: cfDNAPro Version: 1.13.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: 91fabf11b956cfedf9eae31c9ad8e209 NeedsCompilation: no Package: cfTools Version: 1.7.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE MD5sum: 6070453de266f0287ee98d983ef5e7fb NeedsCompilation: yes Package: CGEN Version: 3.43.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: 1f63591c22936fbfbdbf7e798d17e6b1 NeedsCompilation: yes Package: CGHbase Version: 1.67.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: b2643d0f0cf99876157e7d37430d055f NeedsCompilation: no Package: CGHcall Version: 2.69.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: e5d716b07e22c726e0e1f9347358daf6 NeedsCompilation: no Package: cghMCR Version: 1.65.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 1f74e0e05ef75f8825996c329c3d3e51 NeedsCompilation: no Package: CGHnormaliter Version: 1.61.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: de5c2c8249ada1c4efc18e6e7640369f NeedsCompilation: no Package: CGHregions Version: 1.65.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 4e2a33ec6e572cf9f80f4a38008a52e1 NeedsCompilation: no Package: ChAMP Version: 2.37.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: c8f8d3363cccfce3befdbc7fc7e3ae9f NeedsCompilation: no Package: ChemmineOB Version: 1.45.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp, zlibbioc Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit,codetools Enhances: ChemmineR (>= 2.13.0) License: Artistic-2.0 MD5sum: e97b4cd1d3b03fdeef965200bf5b1671 NeedsCompilation: yes Package: ChemmineR Version: 3.59.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 3133086ed179214c122bd7385810c172 NeedsCompilation: yes Package: CHETAH Version: 1.23.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: f3db529da2e143cb8ea256bccca9345b NeedsCompilation: no Package: Chicago Version: 1.35.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: bfdeab4d702443640822233982b39ede NeedsCompilation: no Package: chihaya Version: 1.7.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 159875e93617c25b9e318d0f057074f9 NeedsCompilation: yes Package: chimeraviz Version: 1.33.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 30764fe009171508fd159bddae61af08 NeedsCompilation: no Package: ChIPanalyser Version: 1.29.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: e61b2fa82d18772668b0749e87e56fd2 NeedsCompilation: no Package: ChIPComp Version: 1.37.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 793992737316c9e39138fab2afe340da NeedsCompilation: yes Package: chipenrich Version: 2.31.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: f794ecb39f9255bd06d657f5fb6750d1 NeedsCompilation: no Package: ChIPexoQual Version: 1.31.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 9c367d7079918d30c0005d89167c99a8 NeedsCompilation: no Package: ChIPpeakAnno Version: 3.41.0 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: e640b27b88ae424410e1785bc7dcfd8c NeedsCompilation: no Package: ChIPQC Version: 1.43.0 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: e4b789f16f8ef5bc1eab4a88f48ed0ea NeedsCompilation: no Package: ChIPseeker Version: 1.43.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.1.5) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat License: Artistic-2.0 MD5sum: f097ad1561aeb255ae9c69c8d723337e NeedsCompilation: no Package: chipseq Version: 1.57.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: 402e5d5b322250f32af792ee6ee59610 NeedsCompilation: yes Package: ChIPseqR Version: 1.61.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: 868c03512c0bb7ec22cba01829e214cb NeedsCompilation: yes Package: ChIPsim Version: 1.61.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 0d9c7db033dd65845d01914a8a18eb4d NeedsCompilation: no Package: ChIPXpress Version: 1.51.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8ae3ba698c40243f61d077e750666606 NeedsCompilation: no Package: chopsticks Version: 1.73.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 82f057035f1f0859ae28234b717822fd NeedsCompilation: yes Package: chromDraw Version: 2.37.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: 5f93c5a09f5cd2abfb7d219e60b90bc9 NeedsCompilation: yes Package: ChromHeatMap Version: 1.61.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: e312d4f15f5d76fe08b57ce786ebb15b NeedsCompilation: no Package: chromPlot Version: 1.35.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: f26e33a1db8bda1836f0546bf2c16afa NeedsCompilation: no Package: ChromSCape Version: 1.17.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: 2109a7c4024b47af14005ee54029d091 NeedsCompilation: yes Package: chromVAR Version: 1.29.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: 5fd9aa5a2ca3308e476c46ce6f3e8127 NeedsCompilation: yes Package: CHRONOS Version: 1.35.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: 09dce8670ffea5e682a23cafa15e6b23 NeedsCompilation: no Package: cicero Version: 1.25.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 94a8f62d6981454412a47d08ff7b62de NeedsCompilation: no Package: CIMICE Version: 1.15.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: ae5498d2cf9b8186a417e1ba0260f1a9 NeedsCompilation: no Package: CINdex Version: 1.35.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: e5325bc0639413880ef4de1bbae3ee7a NeedsCompilation: no Package: circRNAprofiler Version: 1.21.0 Depends: R(>= 4.3.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 9492d376fa03e7d5f20d7063592ddf81 NeedsCompilation: no Package: CircSeqAlignTk Version: 1.9.0 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 4ff40c96a2e5525f1a7df9e4435d8133 NeedsCompilation: no Package: cisPath Version: 1.47.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: b629b7b1e2616a5f711e5e8f9432a791 NeedsCompilation: yes Package: CiteFuse Version: 1.19.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 5b22f8d54bdca84382fa5ed9c93e3ebc NeedsCompilation: yes Package: ClassifyR Version: 3.11.0 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale License: GPL-3 MD5sum: c15b2bb2a09ab70337117019c491d29f NeedsCompilation: yes Package: cleanUpdTSeq Version: 1.45.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: ae596e9b89532acd56c89b8307a33ede NeedsCompilation: no Package: CleanUpRNAseq Version: 1.1.1 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, GenomeInfoDb, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: bb6113a1c741d48f2a089a1cf18b0fec NeedsCompilation: no Package: cleaver Version: 1.45.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 86f1c339416015f82933260af9ea8cd7 NeedsCompilation: no Package: clevRvis Version: 1.7.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: e53a540cbd6fff8f9c3cadf60d0d9de8 NeedsCompilation: no Package: clippda Version: 1.57.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 15f983522219f6ebe2ac78f8e3c9050c NeedsCompilation: no Package: clipper Version: 1.47.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: f07dfbf2bc13bf336e50520244f65faa NeedsCompilation: no Package: cliProfiler Version: 1.13.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: aa7249aefa547b15680a24574a8c16eb NeedsCompilation: no Package: cliqueMS Version: 1.21.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: e9f8a1bad3fc05ff19669d3edcdf075b NeedsCompilation: yes Package: Clomial Version: 1.43.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: cdf58efe17351d749ff14391293cf914 NeedsCompilation: no Package: clst Version: 1.55.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 365b3194463e2845e6930fc6b47e4cb5 NeedsCompilation: no Package: clstutils Version: 1.55.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: 6cc7be1c9c0ac6bcad01cf5f1d240afc NeedsCompilation: no Package: CluMSID Version: 1.23.0 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE MD5sum: ccb8461d20794b8776d4fe25aa58cdbf NeedsCompilation: no Package: ClustAll Version: 1.3.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: 6e017319dae1668f1e65b807e1d54d49 NeedsCompilation: no Package: clustComp Version: 1.35.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: fbb81ed42b70cb0f4bd1fed7f2f0d11f NeedsCompilation: no Package: clusterExperiment Version: 2.27.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: d462c13a3acc5ea801a70ed8f72943d5 NeedsCompilation: yes Package: ClusterFoldSimilarity Version: 1.3.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 8c6d5e4cbca500be9db5b3f4d34f9673 NeedsCompilation: no Package: ClusterJudge Version: 1.29.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: a063a662d59224ead16bb61597699466 NeedsCompilation: no Package: clusterProfiler Version: 4.15.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: 70b3ba841eb5a8d5ce1f56a7468921a0 NeedsCompilation: no Package: clusterSeq Version: 1.31.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 9606fb8e65f7f4295efa130ad7991888 NeedsCompilation: no Package: ClusterSignificance Version: 1.35.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 180828de5b8e7302fa5d0f303328413a NeedsCompilation: no Package: clusterStab Version: 1.79.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 19392e3300dff3428f5a78e0430bd8ae NeedsCompilation: no Package: clustifyr Version: 1.19.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: cefad5e60f6637a481c2c436c97dab93 NeedsCompilation: no Package: ClustIRR Version: 1.5.13 Depends: R (>= 4.4.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, pwalign, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: e261cec5f8e704a66af8a980c4794c60 NeedsCompilation: yes Package: CMA Version: 1.65.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 8d31d064263c9630760760b18040c72a NeedsCompilation: no Package: cmapR Version: 1.19.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: 6b2fae7ea3217436c52a6a3df64d44c0 NeedsCompilation: no Package: cn.farms Version: 1.55.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: c79ca82f6b70afecf231da58a86f756b NeedsCompilation: yes Package: cn.mops Version: 1.53.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 4ec460a7d476d3d92a3f7cbe3b052c2a NeedsCompilation: yes Package: CNAnorm Version: 1.53.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 2e8655cb54573cbb88670861a47a189e NeedsCompilation: yes Package: CNEr Version: 1.43.0 Depends: R (>= 3.5.0) Imports: Biostrings (>= 2.33.4), pwalign, DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 44968c337893c92471616e4c4995a154 NeedsCompilation: yes Package: CNORdt Version: 1.49.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 19a2f6f9df4eef59c617526dbe1c32f5 NeedsCompilation: yes Package: CNORfeeder Version: 1.47.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 77260819823417dd703c6727444bb0bf NeedsCompilation: no Package: CNORfuzzy Version: 1.49.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 115431a9454047b57691ec9a305efc56 NeedsCompilation: yes Package: CNORode Version: 1.49.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: ec1d475cbe3074334b7791cc310ed5f8 NeedsCompilation: yes Package: CNTools Version: 1.63.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: 9d71b8f05f6cbf1b627df4fb71662b6a NeedsCompilation: yes Package: CNVfilteR Version: 1.21.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: c407ce29093241682735c7830c19a392 NeedsCompilation: no Package: cnvGSA Version: 1.51.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 70216baf9b83c6db8cda98873d63d44c NeedsCompilation: no Package: CNViz Version: 1.15.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: d4b0bb354932a774411e4e08511c388f NeedsCompilation: no Package: CNVMetrics Version: 1.11.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9b0c28070b9f28f92b89005a252cc4eb NeedsCompilation: no Package: CNVPanelizer Version: 1.39.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 5e071195694f74b7fa1db1a0291f7a33 NeedsCompilation: no Package: CNVRanger Version: 1.23.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: 8d9acb74bfd7e5c6a717057c99257f87 NeedsCompilation: no Package: CNVrd2 Version: 1.45.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 46b5295579d7ba61ac80ed920a86bc8d NeedsCompilation: no Package: CoCiteStats Version: 1.79.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 5e7abfa5f40b15b26d821f87a97d12da NeedsCompilation: no Package: COCOA Version: 2.21.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 0b6499cfd3252e7669def3df1dfcf63c NeedsCompilation: no Package: codelink Version: 1.75.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 91bf478103badb5038f9dc258b7bb76e NeedsCompilation: no Package: CODEX Version: 1.39.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: e0bde123b3e651d0cf5f3dbfe8651ae1 NeedsCompilation: no Package: CoGAPS Version: 3.27.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE MD5sum: 5b2558d10f8cfd0f1e22116aacf42aa6 NeedsCompilation: yes Package: cogena Version: 1.41.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 138e5acd3f1e63c2efff7257f301a554 NeedsCompilation: no Package: cogeqc Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: d3a9c65194ccb0a197e3249ff4c253bd NeedsCompilation: no Package: Cogito Version: 1.13.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 0a7e1de1df4a48cbd571be91e663bb39 NeedsCompilation: no Package: coGPS Version: 1.51.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 4e3629d613c37c64db8589b97fd59b14 NeedsCompilation: no Package: cola Version: 2.13.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 77e1c0e391db425af682aac505fa9ec6 NeedsCompilation: yes Package: comapr Version: 1.11.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 58203ae3e0017da6db666b74258db6a6 NeedsCompilation: no Package: coMethDMR Version: 1.11.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 347d785916496ecade0da58251f7e995 NeedsCompilation: no Package: COMPASS Version: 1.45.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 059d957ef76dca48274d0435f90dbaf9 NeedsCompilation: yes Package: compcodeR Version: 1.43.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 17ef7033e2ea2d39d63316951483bc53 NeedsCompilation: no Package: compEpiTools Version: 1.41.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: a99e47d82a953db9f01925fc3abe1ebe NeedsCompilation: no Package: ComplexHeatmap Version: 2.23.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 0446da886e3ab7b3d190ab7022c5833e NeedsCompilation: no Package: CompoundDb Version: 1.11.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: a52a8b08fb8ccc35e2bf898f5c50b814 NeedsCompilation: no Package: ComPrAn Version: 1.15.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4e214249c74bbe4fd223f79acfee271c NeedsCompilation: no Package: compSPOT Version: 1.5.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3bc6e3c265e9eb3e9019237f0aec72e1 NeedsCompilation: no Package: concordexR Version: 1.7.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 61548ad693c67c7b5531346bcfac6359 NeedsCompilation: no Package: condiments Version: 1.15.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: bef3b0057d130fc9ab4277edd7d71a23 NeedsCompilation: no Package: CONFESS Version: 1.35.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: af15b2223a131cd695ba408dc642890d NeedsCompilation: no Package: consensus Version: 1.25.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: 6dfc91f751969a46ad60ee049bb9ec07 NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.71.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 3349265e3f12d49f470447109b61f2fa NeedsCompilation: no Package: consensusDE Version: 1.25.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 4d001adcc9619a5e927e8626b73fbc51 NeedsCompilation: no Package: consensusSeekeR Version: 1.35.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 4b9f5c30f5d79e4c2cf23cb85e8cb896 NeedsCompilation: no Package: consICA Version: 2.5.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: a71d6b912e70f0fec166c8fc11a12c32 NeedsCompilation: no Package: CONSTANd Version: 1.15.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: 1b4c52e21b37fdde59cb00d2f1532063 NeedsCompilation: no Package: conumee Version: 1.41.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: d249d781f88b23ada3ec6eab15e253bf NeedsCompilation: no Package: convert Version: 1.83.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: b81e19c605a1a673a520cbaa50e86a5f NeedsCompilation: no Package: copa Version: 1.75.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: 1308cacda28659cc583741175183a98d NeedsCompilation: yes Package: CopyNumberPlots Version: 1.23.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 MD5sum: 7dbf406abcb5a55d5b2d680ceb17a128 NeedsCompilation: no Package: coRdon Version: 1.25.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: c01b921d3973e8025df053bce61301f9 NeedsCompilation: no Package: CoreGx Version: 2.11.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: 0e1b81bb4ba70d3a86e7bececd9fbcec NeedsCompilation: no Package: Cormotif Version: 1.53.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: b1747b4b565bb72daec61db971b5889c NeedsCompilation: no Package: corral Version: 1.17.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 MD5sum: 8232ca0692519399f3c70c01cd221139 NeedsCompilation: no Package: coseq Version: 1.31.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 9d60f3fe50b515002cab7c22e9837eb7 NeedsCompilation: no Package: CoSIA Version: 1.7.0 Depends: R (>= 4.3.0), methods (>= 4.3.0), ExperimentHub (>= 2.7.0) Imports: dplyr (>= 1.0.7), magrittr (>= 2.0.1), RColorBrewer (>= 1.1-2), tidyr (>= 1.2.0), plotly (>= 4.10.0), stringr (>= 1.4.0), ggplot2 (>= 3.3.5), tibble (>= 3.1.7), org.Hs.eg.db (>= 3.12.0), org.Mm.eg.db (>= 3.12.0), org.Dr.eg.db (>= 3.12.0), org.Ce.eg.db (>= 3.12.0), org.Dm.eg.db (>= 3.12.0), org.Rn.eg.db (>= 3.12.0), AnnotationDbi (>= 1.52.0), biomaRt (>= 2.46.3), homologene (>= 1.4.68.19), annotationTools (>= 1.64.0), readr (>= 2.1.1), tidyselect (>= 1.1.2), stats (>= 4.1.2) Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) License: MIT + file LICENSE MD5sum: 11b6fd8f582ee4cf33e699cd18a5186f NeedsCompilation: no Package: cosmiq Version: 1.41.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 0878dbb37a7eadf4d11d456460a25c11 NeedsCompilation: yes Package: cosmosR Version: 1.15.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR Suggests: testthat, knitr, rmarkdown, piano, ggplot2 License: GPL-3 MD5sum: 5ac3ea54b12cef10b28513963d509af3 NeedsCompilation: no Package: COSNet Version: 1.41.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 13b6532c3551c2f7eb93fdfd7b411495 NeedsCompilation: yes Package: COTAN Version: 2.7.1 Depends: R (>= 4.3) Imports: stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, dendextend, zeallot, assertthat, withr, SingleCellExperiment, SummarizedExperiment, S4Vectors Suggests: testthat (>= 3.2.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 MD5sum: a81be7a2cc5860ea8807a5ede75efa08 NeedsCompilation: no Package: countsimQC Version: 1.25.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 376604fc69c241e732589a8e1ce4bac5 NeedsCompilation: no Package: covEB Version: 1.33.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: c6fccb6a6b1575a32a15e3c1dba5f14a NeedsCompilation: no Package: CoverageView Version: 1.45.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 12800f8e35fa17d577890926a16d0470 NeedsCompilation: no Package: covRNA Version: 1.33.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: f1cda399cab05324cb42217eaf26f7ab NeedsCompilation: no Package: cpvSNP Version: 1.39.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 288efb00e0a32ab594883f7e6aed7321 NeedsCompilation: no Package: cqn Version: 1.53.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg Suggests: scales, edgeR License: Artistic-2.0 MD5sum: edc24e14bb0377e8ea01b2aa167cf4ba NeedsCompilation: no Package: CRImage Version: 1.55.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 9bed7aaaa326b01d053433a61605cf6b NeedsCompilation: no Package: crisprBase Version: 1.11.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 56280a7a77d5518eda790d6ade5b1fd0 NeedsCompilation: no Package: crisprBowtie Version: 1.11.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 84ee442017cf27cb568ba2cd8a6b3ce2 NeedsCompilation: no Package: crisprBwa Version: 1.11.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: 8700c84502a861f5dc6dc0e54af9b86a NeedsCompilation: no Package: crisprDesign Version: 1.9.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, txdbmaker, utils, VariantAnnotation Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: ccb317fdeef48fb0ce281c58cf547910 NeedsCompilation: no Package: crisprScore Version: 1.11.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8ad0900366dc4839417cbb4e31c1113b NeedsCompilation: no Package: CRISPRseek Version: 1.47.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat License: GPL (>= 2) MD5sum: 065e900a7ffc79da2ae0881602146bdb NeedsCompilation: no Package: crisprShiny Version: 1.3.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: fb8117cd14c2537a4f851a667ea1fc8a NeedsCompilation: no Package: CrispRVariants Version: 1.35.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 16614aef4e1e9473b10f90a6e1cb0bfa NeedsCompilation: no Package: crisprVerse Version: 1.9.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: b37f0da41757af2da8a0501da714b933 NeedsCompilation: no Package: crisprViz Version: 1.9.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: aa9701a8a430094afeb617342fc3af7f NeedsCompilation: no Package: crlmm Version: 1.65.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: 6ea296f1e8785d6b708a2252d3008a4b NeedsCompilation: yes Package: CSAR Version: 1.59.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: ef25f502898ca57975345f02a6ad161b NeedsCompilation: yes Package: csaw Version: 1.41.0 Depends: R (>= 3.5.0), GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 55c2c021b030e8dd5698e1a64a3f3697 NeedsCompilation: yes Package: csdR Version: 1.13.3 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: d9d280eac136bb20a1d0d679113319a0 NeedsCompilation: yes Package: CSSQ Version: 1.19.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: 39349e7e129091c130a2e88de9d72f51 NeedsCompilation: no Package: ctc Version: 1.81.0 Depends: amap License: GPL-2 MD5sum: cdb6d6e5d5c38d19bfa84312444b4acf NeedsCompilation: no Package: CTdata Version: 1.7.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 57472576a9d787b182165170180c68d6 NeedsCompilation: no Package: CTDquerier Version: 2.15.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b55b85b456b8de093160d6d21fd3851b NeedsCompilation: no Package: CTexploreR Version: 1.1.2 Depends: R (>= 4.3), CTdata (>= 1.5.3) Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: 50a93c644ef8f2e1d139f9d3be8b491b NeedsCompilation: no Package: cTRAP Version: 1.25.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: 79b60308ddc324c283f6c40a249ea43e NeedsCompilation: no Package: ctsGE Version: 1.33.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 4773503d4302b596e2660d7ecc6bbf37 NeedsCompilation: no Package: CTSV Version: 1.9.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: b074ec849f6ba7aa4fcbb2ddaac6e3df NeedsCompilation: yes Package: cummeRbund Version: 2.49.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: 1d077049bdbb56c7ad659b1c494cbbf1 NeedsCompilation: no Package: CuratedAtlasQueryR Version: 1.5.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 MD5sum: 110141ee34456ae28fcc1e4b52c6e2e0 NeedsCompilation: no Package: customCMPdb Version: 1.17.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: c69d45b43d8f59f29c2181b8d4055339 NeedsCompilation: no Package: customProDB Version: 1.47.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 8f984d30426ec22018c61ed5257593a5 NeedsCompilation: no Package: cyanoFilter Version: 1.15.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: ed0c631580079d5e35eb08d724362b66 NeedsCompilation: no Package: cycle Version: 1.61.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: c079f6a45d40d08a9587a25d193ade97 NeedsCompilation: no Package: cydar Version: 1.31.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: ac1cf0b54fabbf2c5d0e9da41ef3d74d NeedsCompilation: yes Package: cypress Version: 1.3.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: 0f2d0c3caf6728c436ced1e6eec80710 NeedsCompilation: no Package: CytoDx Version: 1.27.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: a76e2818defebc6ee52d7db89ca05aba NeedsCompilation: no Package: cytofQC Version: 1.7.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: eae97fef9f8d5cad360eab08db0efebc NeedsCompilation: no Package: CytoGLMM Version: 1.15.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 9a982cf44a2bf596af4ebf47a05cbd7c NeedsCompilation: no Package: cytoKernel Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 19ac987980b40a8b3af152f64249d956 NeedsCompilation: yes Package: cytolib Version: 2.19.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: f1ff44367c26145e846cfafb78c60b92 NeedsCompilation: yes Package: cytomapper Version: 1.19.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 72bc35f6b440d126a9e33854b8c7671d NeedsCompilation: no Package: CytoMDS Version: 1.3.1 Depends: R (>= 4.4) Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 0d4f2d23a2546bd905e3d15aeaea7a23 NeedsCompilation: no Package: cytoMEM Version: 1.11.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 6b6b20b55ff738e2d72a61333965a930 NeedsCompilation: no Package: CytoML Version: 2.19.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: f544d1272b12eb55647bb965ecdcb930 NeedsCompilation: yes Package: CytoPipeline Version: 1.7.0 Depends: R (>= 4.4) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI License: GPL-3 MD5sum: 9b9c1c2ebaf363445d3211f740a84dea NeedsCompilation: no Package: CytoPipelineGUI Version: 1.5.0 Depends: R (>= 4.4), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: e82fb0ecbb5cb5f48ba97ae619db8923 NeedsCompilation: no Package: cytoviewer Version: 1.7.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 387a359545f6a1d55d1aceaf1ab1da9d NeedsCompilation: no Package: dada2 Version: 1.35.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: d767058a803a99a0088bcdc1b36d0a0b NeedsCompilation: yes Package: dagLogo Version: 1.45.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: ca53899791ab56a7ec86040840135b5b NeedsCompilation: no Package: daMA Version: 1.79.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 6e4f9cd46aede1142190567da6366c7a NeedsCompilation: no Package: DAMEfinder Version: 1.19.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: f6b04e6869776783be1f6b7d096b5020 NeedsCompilation: no Package: DaMiRseq Version: 2.19.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: a0f37a727c6ec9e1a4da2479ef478c5a NeedsCompilation: no Package: Damsel Version: 1.3.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: e70cdd63daa72624366351094f6647bf NeedsCompilation: no Package: DAPAR Version: 1.39.0 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 4a962ed160ce46e3fa72e9d6a9fdf327 NeedsCompilation: no Package: DART Version: 1.55.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 36a2a2fcff52bb2bf06ce58191b633de NeedsCompilation: no Package: dcanr Version: 1.23.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 8d6ed7913505b790d657ee2838168868 NeedsCompilation: no Package: DCATS Version: 1.5.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 1faa56842660f648d975a7435404ab5e NeedsCompilation: no Package: dce Version: 1.13.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: a369874285bc5f4d10415002ecdc1f03 NeedsCompilation: no Package: dcGSA Version: 1.35.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 8b69f62dae97659decd1474bf8dc025a NeedsCompilation: no Package: ddCt Version: 1.63.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: 504a29359b77f2c92062c045efc9ccd8 NeedsCompilation: no Package: ddPCRclust Version: 1.27.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: fcbab27498957051a01a8cfd2d6bdd08 NeedsCompilation: no Package: dearseq Version: 1.19.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: d844621512866203027e15927a6ae97d NeedsCompilation: no Package: debCAM Version: 1.25.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 5a9e48ce4f179d28d875fcf6934a5c8f NeedsCompilation: no Package: debrowser Version: 1.35.0 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: a507a1fa8f86e785267477165496caaa NeedsCompilation: no Package: DECIPHER Version: 3.3.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: ac25cf30c0c35f0bb22022eca7c15070 NeedsCompilation: yes Package: decompTumor2Sig Version: 2.23.0 Depends: R(>= 4.0), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 62e274e3d8f966ccd7083d3209ee96ec NeedsCompilation: no Package: DeconRNASeq Version: 1.49.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: ffe78f38b7c3ff729592fb67d6863f24 NeedsCompilation: no Package: decontam Version: 1.27.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 7ac6c33f8479c403a0c1f20f6861f2b4 NeedsCompilation: no Package: decontX Version: 1.5.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bb83b24c89c91b8693aa68bed709e0ae NeedsCompilation: yes Package: decoupleR Version: 2.13.0 Depends: R (>= 4.0) Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick License: GPL-3 + file LICENSE MD5sum: b062e20601a2d330e2a75b63cb7c56c2 NeedsCompilation: no Package: DeepPINCS Version: 1.15.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 9b9c27503b422628bfaf8f426062b3fc NeedsCompilation: no Package: deepSNV Version: 1.53.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: a66619f626641914eacc934bd78c3126 NeedsCompilation: yes Package: DeepTarget Version: 1.1.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: b47b6fabcd4147b8f5e8b2f50c9ec4ba NeedsCompilation: no Package: DEFormats Version: 1.35.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: 54bcb46a47b211c2be35f0279b5f98be NeedsCompilation: no Package: DegCre Version: 1.3.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 53dd1a5436d63aef7abdbe68af6231ca NeedsCompilation: no Package: DegNorm Version: 1.17.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: a270193c5a572ef23c5e4f5507f920ad NeedsCompilation: yes Package: DEGraph Version: 1.59.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: ffc8b9f4519a263767159b1f9372e139 NeedsCompilation: no Package: DEGreport Version: 1.43.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 867aaed2658d76b50baa36f5492074d2 NeedsCompilation: no Package: DEGseq Version: 1.61.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: eefebb29199988229ea722e8d7759939 NeedsCompilation: yes Package: DelayedArray Version: 0.33.2 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>= 1.5.42) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 680c8b19ba2a8aac3453561fb24dfd6a NeedsCompilation: yes Package: DelayedDataFrame Version: 1.23.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: aa4af3adaf7326d0ed26d2e320ca864b NeedsCompilation: no Package: DelayedMatrixStats Version: 1.29.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>= 1.5.19) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: 321110b0bba988b8aa287257c23a1bff NeedsCompilation: no Package: DelayedRandomArray Version: 1.15.0 Depends: SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 2d3c6f79e034dd9e1809382d6cd8a0cd NeedsCompilation: yes Package: DelayedTensor Version: 1.13.0 Depends: R (>= 4.1.0) Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: c2708e6eab7fa0e20accee421c0d3116 NeedsCompilation: no Package: DELocal Version: 1.7.0 Imports: DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2, matrixStats, stats Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle License: MIT + file LICENSE MD5sum: 6f70db054ef9559d18011b75f96f899d NeedsCompilation: no Package: deltaCaptureC Version: 1.21.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 906a86248863e4b8cadcc85421302d3c NeedsCompilation: no Package: deltaGseg Version: 1.47.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: b0aaec8022fe71ee6b63e03006d0fe0f NeedsCompilation: no Package: DeMAND Version: 1.37.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: f7b6b188d3d60f7a336c680b767601ff NeedsCompilation: no Package: DeMixT Version: 1.23.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 45925f5de82015e41f7daf8d1cb783f4 NeedsCompilation: yes Package: demuxmix Version: 1.9.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 33a16f9d3f8904d577533fa81e5513ad NeedsCompilation: no Package: demuxSNP Version: 1.5.0 Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports: MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat License: GPL-3 MD5sum: 9f3c3723cc7f3284256bda2e68cf5f1c NeedsCompilation: no Package: densvis Version: 1.17.0 Imports: Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat License: MIT + file LICENSE MD5sum: b377783448749a39b9503547d67058be NeedsCompilation: yes Package: DEP Version: 1.29.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 034d1a7a29c1259dd8ebf6245721a0ff NeedsCompilation: no Package: DepecheR Version: 1.23.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: d631e6d53a21f8deda581c7b425ce05f NeedsCompilation: yes Package: DepInfeR Version: 1.11.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm License: GPL-3 MD5sum: 77423bf73f100a9bcfa5ac7085169be5 NeedsCompilation: no Package: DEqMS Version: 1.25.0 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 10ce878650a4980d9f0c2d86d60f34cf NeedsCompilation: no Package: DEScan2 Version: 1.27.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: abac8e353578145f5909d40f4fdad9ca NeedsCompilation: yes Package: DESeq2 Version: 1.47.1 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: e1fda65b18b39ec278dd0cfc7d9506de NeedsCompilation: yes Package: DEsingle Version: 1.27.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 814f7f28c08dc3ef74ca533d4f359bd1 NeedsCompilation: no Package: DESpace Version: 1.7.0 Depends: R (>= 4.3.0) Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, ggpubr, scales, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel, methods Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils License: GPL-3 MD5sum: 9d825aa7eb388e5718d6fd522579486e NeedsCompilation: no Package: destiny Version: 3.21.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 MD5sum: a2a7e04846f826461005fca7b86ba56b NeedsCompilation: yes Package: DEsubs Version: 1.33.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: 7482de722eeb342c9260cc190dacba9b NeedsCompilation: no Package: DEWSeq Version: 1.21.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: d2871376b909562c5dfbbde475c44038 NeedsCompilation: no Package: DExMA Version: 1.15.0 Depends: R (>= 4.1), DExMAdata Imports: Biobase, GEOquery, impute, limma, pheatmap, plyr, scales, snpStats, sva, swamp, stats, methods, utils, bnstruct, RColorBrewer, grDevices Suggests: BiocStyle, qpdf, BiocGenerics, RUnit License: GPL-2 MD5sum: f2fba0b54ad74ec858b2416c0e2a9d8a NeedsCompilation: no Package: DFP Version: 1.65.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: 43ae91652af37f4fccf82df9d3083404 NeedsCompilation: no Package: DFplyr Version: 1.1.0 Depends: dplyr Imports: BiocGenerics, methods, rlang, S4Vectors, tidyselect Suggests: BiocStyle, GenomeInfoDb, GenomicRanges, IRanges, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), tibble License: GPL-3 MD5sum: 1ef95960b26acdafe17983cf70bbde94 NeedsCompilation: no Package: DiffBind Version: 3.17.0 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: 1acfa441f9dc0c5f9f9c0edfdc8cebb7 NeedsCompilation: yes Package: diffcoexp Version: 1.27.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: cf939b233c0dac583cea3d983c38aff4 NeedsCompilation: no Package: diffcyt Version: 1.27.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: eeca3698a9eaf140653033965d034f5b NeedsCompilation: no Package: DifferentialRegulation Version: 2.5.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 36e977958c3e1e23013c3f3b38872253 NeedsCompilation: yes Package: diffGeneAnalysis Version: 1.89.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 7d75d52a1424532b6ce561b33bfa0894 NeedsCompilation: no Package: diffHic Version: 1.39.0 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: 8807ae8a8ede83cfb457edf5924c9a6a NeedsCompilation: yes Package: DiffLogo Version: 2.31.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: adcf5ba9d4beca94614d75128f3af703 NeedsCompilation: no Package: diffuStats Version: 1.27.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils License: GPL-3 MD5sum: f654b32696e6377036c61ecd5a983910 NeedsCompilation: yes Package: diggit Version: 1.39.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: d9922171ff24749c3baf83676c272561 NeedsCompilation: no Package: Dino Version: 1.13.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: b91dcfe0bdea54f9e11a651daa96e00c NeedsCompilation: no Package: dinoR Version: 1.3.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 228edc55576b1c5285b00e67f0413dd8 NeedsCompilation: no Package: dir.expiry Version: 1.15.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: 8de15560fbcd2b1d639c5ee0b836c098 NeedsCompilation: no Package: Director Version: 1.33.0 Depends: R (>= 4.0) Imports: htmltools, utils, grDevices License: GPL-3 + file LICENSE MD5sum: f1efbb93767cc1edac8c08e34c79f087 NeedsCompilation: no Package: DirichletMultinomial Version: 1.49.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 8bc79040f15522671a6e389d2dd9d382 NeedsCompilation: yes Package: discordant Version: 1.31.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 38398e7f1ec6460034588e43e091245d NeedsCompilation: yes Package: DiscoRhythm Version: 1.23.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: 347eb7f593ffb6f5c5303992d5c06470 NeedsCompilation: no Package: distinct Version: 1.19.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: 63a3b0ed24cc1214e69100dbd71f6189 NeedsCompilation: yes Package: dittoSeq Version: 1.19.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE MD5sum: 7a7d0203aff164b521fc73203bf6c67b NeedsCompilation: no Package: divergence Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: a9d2f36a82c152f847a183ef9e72c1ca NeedsCompilation: no Package: dks Version: 1.53.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 92a497c5055c5637e5c1d5e515654ba3 NeedsCompilation: no Package: DMCFB Version: 1.21.0 Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges Imports: utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: e79afca1aa5471d1baadcb7bb1f6d4d2 NeedsCompilation: no Package: DMCHMM Version: 1.29.0 Depends: R (>= 4.1.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool Imports: utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: bae753a2f5f3cafc1e4c36e655ddba86 NeedsCompilation: no Package: DMRcaller Version: 1.39.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 819431e473505cab31a0f8f4e70629af NeedsCompilation: no Package: DMRcate Version: 3.3.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: e334c0513220dc51eb9b57aa7ffbce1f NeedsCompilation: no Package: dmrseq Version: 1.27.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 8b6eff5f6dce9ecc2873c58d938eed38 NeedsCompilation: no Package: DNABarcodeCompatibility Version: 1.23.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 20e9daec0e78088b5d751c8dbb81912f NeedsCompilation: yes Package: DNABarcodes Version: 1.37.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: cc7e4318d686a7875a8a28486082e4e0 NeedsCompilation: yes Package: DNAcopy Version: 1.81.0 License: GPL (>= 2) MD5sum: fc6cac7f73017c8148f7d12f64f76aaf NeedsCompilation: yes Package: DNAfusion Version: 1.9.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 3e97235bbc3b7d7c9fbc50f7b970789f NeedsCompilation: no Package: DNAshapeR Version: 1.35.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: b738a616d0475594a94b8959702b98ed NeedsCompilation: yes Package: DominoEffect Version: 1.27.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 215d286429324a0ef85f364e17ba890a NeedsCompilation: no Package: dominoSignal Version: 1.1.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 7e87bc7f76a17696f7dd4f0ba471de9e NeedsCompilation: no Package: doppelgangR Version: 1.35.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: 45b4f71a9c59d512e32d61984907348f NeedsCompilation: no Package: Doscheda Version: 1.29.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 071c4ec8871c7fe965fa78607f4525c4 NeedsCompilation: no Package: DOSE Version: 4.1.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9141c32d267c2d1e45095490348bd546 NeedsCompilation: no Package: doseR Version: 1.23.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: c2109bc5e0b7e49fc9ca57d93d9f7596 NeedsCompilation: no Package: doubletrouble Version: 1.7.0 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: f6ef3c50e3b971f05257f2f66336ce51 NeedsCompilation: no Package: drawProteins Version: 1.27.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 935d75853df050f5a744bad0dd7d516e NeedsCompilation: no Package: dreamlet Version: 1.5.0 Depends: R (>= 4.3.0), variancePartition (>= 1.33.11), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle License: Artistic-2.0 MD5sum: 64e0536c54b223d0606cdb3cb89fc04f NeedsCompilation: yes Package: DRIMSeq Version: 1.35.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 8a625cf608e725315651690307d2e9e0 NeedsCompilation: no Package: DriverNet Version: 1.47.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: 5de66b21ba86c160a6fd6769b7aa0bcd NeedsCompilation: no Package: DropletUtils Version: 1.27.0 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: 24cf1048d010f220bdf07cb2911ca236 NeedsCompilation: yes Package: drugTargetInteractions Version: 1.15.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: 5d8be70766cd4f6bb9bb405e08d0bc00 NeedsCompilation: no Package: DrugVsDisease Version: 2.49.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 MD5sum: bbe8b86958c3e739fccedd85bd652d7a NeedsCompilation: no Package: DSS Version: 2.55.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: 672b711143db263aef806d6733ba75ff NeedsCompilation: yes Package: dStruct Version: 1.13.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 8890f0c7e8384e1e5ee6a78f17b6d491 NeedsCompilation: no Package: DTA Version: 2.53.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: 1582cef58372e425bb8732a036e7a966 NeedsCompilation: no Package: Dune Version: 1.19.0 Depends: R (>= 3.6) Imports: BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr, tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode Suggests: knitr, rmarkdown, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 469581728c1a9070af78518ebca71180 NeedsCompilation: no Package: DuplexDiscovereR Version: 1.1.0 Depends: R (>= 4.4), InteractionSet Imports: Gviz, Biostrings, rtracklayer, GenomicAlignments, GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr, tibble, tidyr, purrr, methods, grDevices, stats, utils Suggests: knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: c9ff3e6dbec14fa10f50447c54ca095d NeedsCompilation: no Package: dupRadar Version: 1.37.0 Depends: R (>= 3.2.0) Imports: Rsubread (>= 1.14.1), KernSmooth Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub License: GPL-3 MD5sum: c90e148780dae1051ad7153e868bef3d NeedsCompilation: no Package: dyebias Version: 1.67.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 MD5sum: 933ca5288ff17d17d76952f9da9cda9d NeedsCompilation: no Package: DynDoc Version: 1.85.0 Depends: methods, utils Imports: methods License: Artistic-2.0 MD5sum: b802c3d469d9f5fd94ad4073a8dd1b98 NeedsCompilation: no Package: easier Version: 1.13.0 Depends: R (>= 4.2.0) Imports: progeny, easierData, dorothea (>= 1.6.0), decoupleR, quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang, BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper License: MIT + file LICENSE MD5sum: 21842e3166ea7bbdfbc679475b71edbb NeedsCompilation: no Package: EasyCellType Version: 1.9.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>= 0.6.4), BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle License: Artistic-2.0 MD5sum: 18fb6a1f24cdb6fd5cf2b95bbef18f8b NeedsCompilation: no Package: easylift Version: 1.5.0 Depends: GenomicRanges, BiocFileCache Imports: rtracklayer, GenomeInfoDb, R.utils, tools, methods Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: af65b22b32498b63c0a920611bff70ba NeedsCompilation: no Package: easyreporting Version: 1.19.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 3cee64fa0654e5d7e6a1cd6ff1bc5717 NeedsCompilation: no Package: easyRNASeq Version: 2.43.0 Imports: Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics (>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1), Biostrings (>= 2.72.1), edgeR (>= 4.2.1), GenomeInfoDb (>= 1.40.1), genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.40.0), GenomicRanges (>= 1.56.1), SummarizedExperiment (>= 1.34.0), graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0), methods, parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.20.0), S4Vectors (>= 0.42.1), ShortRead (>= 1.62.0), utils Suggests: BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33) License: Artistic-2.0 MD5sum: ae7b560cb851f0aaa2434bed507c2003 NeedsCompilation: no Package: EBarrays Version: 2.71.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: 844beddb438532c29a8da6bc00c53498 NeedsCompilation: yes Package: EBcoexpress Version: 1.51.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: b40535a5279edc92df3b541d69da44b5 NeedsCompilation: yes Package: EBImage Version: 4.49.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: 2fb13cb9b0acedabee242aae27ebfde6 NeedsCompilation: yes Package: EBSEA Version: 1.35.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 MD5sum: bbd1e1144c92bdb4472877b4dc09e5b8 NeedsCompilation: no Package: EBSeq Version: 2.5.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0) LinkingTo: Rcpp,RcppEigen,BH License: Artistic-2.0 MD5sum: 44b18bb410e3689daf341f86e0071ebf NeedsCompilation: yes Package: ecolitk Version: 1.79.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: 7f2b281de463d6f765a678230b0de291 NeedsCompilation: no Package: EDASeq Version: 2.41.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 MD5sum: eddb6c6de525dcb3c56a13b682eea9a6 NeedsCompilation: no Package: edge Version: 2.39.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: dbed0bf91790338911dc048ce00641ca NeedsCompilation: yes Package: edgeR Version: 4.5.0 Depends: R (>= 3.6.0), limma (>= 3.61.9) Imports: methods, graphics, stats, utils, locfit Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject License: GPL (>= 2) MD5sum: 47f8b118673f6d39c8d66adfbdb84c4e NeedsCompilation: yes Package: EDIRquery Version: 1.7.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: aca8b76dd94c493cf6639e75c1827145 NeedsCompilation: no Package: eds Version: 1.9.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: a222a8466fd5c23685395d8a47b63f03 NeedsCompilation: yes Package: EGAD Version: 1.35.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 MD5sum: 7364c6d2370e1ec73ee96a12f4898d12 NeedsCompilation: no Package: EGSEA Version: 1.35.0 Depends: R (>= 4.3.0), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 652146426f4da9f7a18ac171137e1518 NeedsCompilation: no Package: eiR Version: 1.47.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite License: Artistic-2.0 MD5sum: 2a8dd46b295784556bd3a13e2e23ff8b NeedsCompilation: yes Package: eisaR Version: 1.19.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer License: GPL-3 MD5sum: cee013ad7592666590e492b498defb7b NeedsCompilation: no Package: ELMER Version: 2.31.0 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: eac9ad812c49757fa74ccb07d72ff339 NeedsCompilation: no Package: EMDomics Version: 2.37.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: 45681860bf8d9c9364cb4ba03999d0b8 NeedsCompilation: no Package: EmpiricalBrownsMethod Version: 1.35.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 2ac0d9bd7a5d53286c2d235669a255b5 NeedsCompilation: no Package: EnhancedVolcano Version: 1.25.0 Depends: ggplot2, ggrepel Imports: methods Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 MD5sum: be827e677511fbbd2aeb29bf3110daef NeedsCompilation: no Package: enhancerHomologSearch Version: 1.13.1 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) MD5sum: 21b31a0dcf40e99914ed18c5de01395d NeedsCompilation: yes Package: EnMCB Version: 1.19.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: 115608284ef76981ca7edc3067aca08f NeedsCompilation: no Package: ENmix Version: 1.43.1 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 52f0205095cb2bddd120a755cb296179 NeedsCompilation: no Package: EnrichDO Version: 1.1.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, Rgraphviz, clusterProfiler, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, readr, stringr, tidyr, grDevices, stats, RColorBrewer Suggests: knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: cc513c5ca394d10cc8b04eca44b2bf50 NeedsCompilation: no Package: EnrichedHeatmap Version: 1.37.0 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 4c2c644daf9ec8f4dfa8b53aecc3cf79 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.37.0 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: b99ec3f4af1dbbca85ed27e822948cb1 NeedsCompilation: no Package: enrichplot Version: 1.27.1 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2, ggrepel (>= 0.9.0), ggtangle (>= 0.0.4), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: 109587ba42c597c09045d650ffc61610 NeedsCompilation: no Package: enrichViewNet Version: 1.5.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick License: Artistic-2.0 MD5sum: bed8197731a8b8d52b0dd546efdd59eb NeedsCompilation: no Package: ensembldb Version: 2.31.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: cc0c3b5af780df595713644ad36a0dcb NeedsCompilation: no Package: epialleleR Version: 1.15.1 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: e28f7acd21d27b9f091d33b1f3a27e16 NeedsCompilation: yes Package: EpiCompare Version: 1.11.0 Depends: R (>= 4.2.0) Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis License: GPL-3 MD5sum: 5ad7c2754505af5391abba542cdd42b7 NeedsCompilation: no Package: epidecodeR Version: 1.15.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 110d6263f49ca2fc1fd37b817180e819 NeedsCompilation: no Package: EpiDISH Version: 2.23.1 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 31ba6a7dc7c1bf5904d6b9ba13154405 NeedsCompilation: no Package: epigenomix Version: 1.47.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: c1c8152a61c4c779d2682db6ad7373e7 NeedsCompilation: no Package: epigraHMM Version: 1.15.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 0e85fd394d77a5e1684fd675387d6cc1 NeedsCompilation: yes Package: EpiMix Version: 1.9.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 3e493ced5bc2ab34dab0301693c3a12e NeedsCompilation: no Package: epimutacions Version: 1.11.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 3b139888cb6d8d8bfc12f55729a25eaa NeedsCompilation: yes Package: epiNEM Version: 1.31.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: ecb80a0c5c040677b87a82f5df5b9a99 NeedsCompilation: no Package: EpipwR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: e18f3eae20a1c90e2185739208b8bfbd NeedsCompilation: no Package: epiregulon Version: 1.3.0 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, beachmat.hdf5 License: MIT + file LICENSE MD5sum: 758802556a89c75052720e68171d3b14 NeedsCompilation: yes Package: epiregulon.extra Version: 1.3.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: 9d8b99f64ef6ccbba39f3d6ba76d5d0a NeedsCompilation: no Package: epistack Version: 1.13.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 4fe2007e8a3a5219e937f574ce839987 NeedsCompilation: no Package: epistasisGA Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: eaa51002720a5d4f3b2e4f071a9ed4a8 NeedsCompilation: yes Package: EpiTxDb Version: 1.19.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 37b0707c145961ac3d61bdd9aa073432 NeedsCompilation: no Package: epivizr Version: 2.37.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 146b736e811b17d71e0877d27069811e NeedsCompilation: no Package: epivizrChart Version: 1.29.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: e59a113e0396dcb233c1eacefcd0bb33 NeedsCompilation: no Package: epivizrData Version: 1.35.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: dd767cfce4b72d751c4a911d0f880c50 NeedsCompilation: no Package: epivizrServer Version: 1.35.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: f71c0e0802fd906a9585b087585fa6a4 NeedsCompilation: no Package: epivizrStandalone Version: 1.35.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: 9d327d681d5c95be00f790dc1699711d NeedsCompilation: no Package: erccdashboard Version: 1.41.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 90ca6a92236ef5e17be6cce4b48fbb1e NeedsCompilation: no Package: erma Version: 1.23.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: c9321d28f6f8d63eb0b931af03a3f1f6 NeedsCompilation: no Package: ERSSA Version: 1.25.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 0f93d4ccb606a9742da91832aec42e63 NeedsCompilation: no Package: esATAC Version: 1.29.0 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: 53d1c1e27d82624f135ff31aa35ba99f NeedsCompilation: yes Package: escape Version: 2.3.0 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 3a8549a14c3930ae5df297f3813d72e7 NeedsCompilation: no Package: escheR Version: 1.7.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 6c6b1f456e96392582fdc25e12cfa86a NeedsCompilation: no Package: esetVis Version: 1.33.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: a7a2593f81e68ecaa4f63134e69b7b82 NeedsCompilation: no Package: eudysbiome Version: 1.37.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 29232592154e028bfecf74ee3d043260 NeedsCompilation: no Package: evaluomeR Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 7f35c5e339a0764bfeed7433cd9137ff NeedsCompilation: no Package: EventPointer Version: 3.15.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: c4f7f8128c0d830799b4c4f13915f9b4 NeedsCompilation: yes Package: EWCE Version: 1.15.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: 10f525b27828ef1053ed9876e12408db NeedsCompilation: no Package: ExCluster Version: 1.25.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: d644973362555239eb94a7e45af0d753 NeedsCompilation: no Package: ExiMiR Version: 2.49.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 MD5sum: eb76e2b35dac49e6cf07656891c13a83 NeedsCompilation: no Package: ExperimentHub Version: 2.15.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: e937c1b2175175ea0f5bc0821b6275e6 NeedsCompilation: no Package: ExperimentHubData Version: 1.33.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: f59c22bba53e21b309f77e18dd443ff0 NeedsCompilation: no Package: ExperimentSubset Version: 1.17.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: 3476fc9334c565b2acb699bb85215539 NeedsCompilation: no Package: ExploreModelMatrix Version: 1.19.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: 674f43803b15b909ad14dfce07ae17a8 NeedsCompilation: no Package: ExpressionAtlas Version: 1.35.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 09ba95f3fdcf829380ebd84da9b7dbd1 NeedsCompilation: no Package: extraChIPs Version: 1.11.0 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble Imports: BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, GenomicAlignments, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram Suggests: apeglm, BiocStyle, covr, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 090f03599f2f243e332e8d8c18f6bef9 NeedsCompilation: yes Package: fabia Version: 2.53.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 6f88996bb803626d6b467569484b3ce4 NeedsCompilation: yes Package: factDesign Version: 1.83.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: bc9f865a0992acc847d3be2ff52cf188 NeedsCompilation: no Package: factR Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocGenerics (>= 0.46), Biostrings (>= 2.68), GenomeInfoDb (>= 1.36), dplyr (>= 1.1), GenomicFeatures (>= 1.52), GenomicRanges (>= 1.52), IRanges (>= 2.34), purrr (>= 1.0), rtracklayer (>= 1.60), tidyr (>= 1.3), methods (>= 4.3), BiocParallel (>= 1.34), S4Vectors (>= 0.38), data.table (>= 1.14), rlang (>= 1.1), tibble (>= 3.2), wiggleplotr (>= 1.24), RCurl (>= 1.98), XML (>= 3.99), drawProteins (>= 1.20), ggplot2 (>= 3.4), stringr (>= 1.5), pbapply (>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3), crayon (>= 1.5) Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork License: file LICENSE MD5sum: 8de097d63ba83be56f44f612a5bd6995 NeedsCompilation: no Package: faers Version: 1.3.0 Depends: R (>= 3.5.0) Imports: BiocParallel, brio, cli, curl (>= 5.0.0), data.table, httr2 (>= 1.0.0), MCMCpack, methods, openEBGM, rlang (>= 1.1.0), rvest, tools, utils, vroom, xml2 Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c659ef70405a1b857be76f4dce0bf4f5 NeedsCompilation: no Package: FamAgg Version: 1.35.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE MD5sum: 682aa0a5035619b1f74690d3a0d09ed7 NeedsCompilation: no Package: famat Version: 1.17.0 Depends: R (>= 4.0) Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 MD5sum: 1fc08d15147121d5eb1f202772106df0 NeedsCompilation: no Package: fastLiquidAssociation Version: 1.43.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: c996aa12578383ae42e455c1c742fbdd NeedsCompilation: no Package: FastqCleaner Version: 1.25.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0d04173e47e0b2486ca4ab67d51df272 NeedsCompilation: yes Package: fastreeR Version: 1.11.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: b599d5d7903295ab2aa4c4789d92c9dc NeedsCompilation: no Package: fastseg Version: 1.53.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo, BiocStyle, knitr License: LGPL (>= 2.0) MD5sum: 8ded0838ce690413637c5390100675c4 NeedsCompilation: yes Package: fCCAC Version: 1.33.0 Depends: R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b0eca5ee92acc13b0201d00211388ed6 NeedsCompilation: no Package: fCI Version: 1.37.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: f1ee633226c453188dc69b085d214810 NeedsCompilation: no Package: fcScan Version: 1.21.0 Imports: stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8acd48c61ad91b0a91f0df8a849a4c11 NeedsCompilation: no Package: fdrame Version: 1.79.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 161d5e89b1a0b09b7f980909eab8d915 NeedsCompilation: yes Package: FEAST Version: 1.15.0 Depends: R (>= 4.1), mclust, BiocParallel, SummarizedExperiment Imports: SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 2d1a2bf5cc520ae800a334356b8e4c0d NeedsCompilation: yes Package: FeatSeekR Version: 1.7.0 Imports: pheatmap, MASS, pracma, stats, SummarizedExperiment, methods Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) License: GPL-3 MD5sum: d677b68a81f93bdd4114ebf9bdb7f5af NeedsCompilation: no Package: fedup Version: 1.15.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE MD5sum: f99a7f5d80e5f8a428934551f48721b0 NeedsCompilation: no Package: FELLA Version: 1.27.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 6746a4f3dc2949cd600dcd7a5dc6154a NeedsCompilation: no Package: fenr Version: 1.5.0 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE MD5sum: 9d9a921be969c9c87d12c578bcd577f3 NeedsCompilation: no Package: ffpe Version: 1.51.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 8fe98a07b548c031c65ff2581ce583b3 NeedsCompilation: no Package: fgga Version: 1.15.0 Depends: R (>= 4.3), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle License: GPL-3 MD5sum: 82c13438996d2226e908550f702bdeec NeedsCompilation: no Package: FGNet Version: 3.41.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) MD5sum: 296bb447f054a159036041ac14debaa1 NeedsCompilation: no Package: fgsea Version: 1.33.0 Depends: R (>= 4.1) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat License: MIT + file LICENCE MD5sum: 979527736c5b26df608f05d54436d09d NeedsCompilation: yes Package: FilterFFPE Version: 1.17.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 MD5sum: 95b123bc3a68ee984bd769e45d91b124 NeedsCompilation: no Package: findIPs Version: 1.3.0 Depends: graphics, R (>= 4.4.0) Imports: Biobase, BiocParallel, parallel, stats, SummarizedExperiment, survival, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7aebf019184d051faab8b664abb11cf3 NeedsCompilation: no Package: FindIT2 Version: 1.13.0 Depends: GenomicRanges, R (>= 3.5.0) Imports: withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors, GenomicFeatures, dplyr, rlang, patchwork, ggplot2, BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 License: Artistic-2.0 MD5sum: 0a6681e6670668ad7b6148d15007c16c NeedsCompilation: no Package: FISHalyseR Version: 1.41.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: 78b4d81d5aabf926774d3630e118e6a0 NeedsCompilation: no Package: fishpond Version: 2.13.0 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table License: GPL-2 MD5sum: e20339fe0e023b304ef15f4525418f04 NeedsCompilation: no Package: FitHiC Version: 1.33.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 77f4113d1dd1bebcfb0b6a79964b17e3 NeedsCompilation: yes Package: flagme Version: 1.63.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 591c172145b311782550652a081ff340 NeedsCompilation: yes Package: FLAMES Version: 2.1.1 Depends: R (>= 4.1.0) Imports: basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, txdbmaker, GenomicAlignments, GenomeInfoDb, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, Matrix, MatrixGenerics, parallel, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, future, methods, tibble, tidyselect, IRanges LinkingTo: Rcpp, Rhtslib, testthat Suggests: BiocStyle, GEOquery, knitr, rmarkdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2 License: GPL (>= 3) MD5sum: 5e7213194338e98c0eb601848b12a4e2 NeedsCompilation: yes Package: flowAI Version: 1.37.0 Depends: R (>= 4.3.0) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) MD5sum: aa15855427ebd549be0f2ace4824d8a4 NeedsCompilation: no Package: flowBeads Version: 1.45.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 2f63d77151964c63750f7d7530c54a0f NeedsCompilation: no Package: flowBin Version: 1.43.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: f169c6bcf9a0e52c910a6c3724ce992d NeedsCompilation: no Package: flowcatchR Version: 1.41.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: da792ef02f06f51f4ae0995cf7581262 NeedsCompilation: no Package: flowCHIC Version: 1.41.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 MD5sum: e5cbe7d93d74ff61e7d1067b4574e905 NeedsCompilation: no Package: flowClean Version: 1.45.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 MD5sum: 3cf491041e7731167da60244d31a92fa NeedsCompilation: no Package: flowClust Version: 3.45.0 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, flowCore, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) License: MIT MD5sum: 57819f2b9b3b23e073714c8bd6cf28af NeedsCompilation: yes Package: flowCore Version: 2.19.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>= 2.13.1), S4Vectors LinkingTo: cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 MD5sum: 8a3b99be4b7fba3f88b1188adb7f6b8a NeedsCompilation: yes Package: flowCut Version: 1.17.0 Depends: R (>= 3.4), flowCore Imports: flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics, stats,methods Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown License: Artistic-2.0 MD5sum: 93d8aa49eeba59903cc361bd17c37b03 NeedsCompilation: no Package: flowCyBar Version: 1.43.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: 271f0dc9f3e3c45ab610787efb57aac5 NeedsCompilation: no Package: flowDensity Version: 1.41.0 Imports: flowCore, graphics, flowViz (>= 1.42), car, polyclip, gplots, methods, stats, grDevices Suggests: knitr,rmarkdown License: Artistic-2.0 MD5sum: 2d73b52b7ae3ade91d2388ae8973733c NeedsCompilation: no Package: flowFP Version: 1.65.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 MD5sum: 8960d5dd75c50f0bfb78b56d40df4d43 NeedsCompilation: yes Package: flowGate Version: 1.7.0 Depends: flowWorkspace (>= 4.0.6), ggcyto (>= 1.16.0), R (>= 4.2) Imports: shiny (>= 1.5.0), BiocManager (>= 1.30.10), flowCore (>= 2.0.1), dplyr (>= 1.0.0), ggplot2 (>= 3.3.2), rlang (>= 0.4.7), purrr, tibble, methods Suggests: knitr, rmarkdown, stringr, tidyverse, testthat License: MIT + file LICENSE MD5sum: ef344f078f9cfd659489233cd4308d4c NeedsCompilation: no Package: flowGraph Version: 1.15.0 Depends: R (>= 4.1) Imports: effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2, igraph, Matrix, matrixStats, stats, utils, visNetwork, htmlwidgets, grDevices, methods, stringr, stringi, Rdpack, data.table (>= 1.9.5), gridExtra, Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 9aa6068aa8cf283d729cba4f4c0d23ea NeedsCompilation: no Package: flowMatch Version: 1.43.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: aafae8ac42f571d3ddee11b18cf8504f NeedsCompilation: yes Package: flowMeans Version: 1.67.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: e57e6b9cfe2dd6923cf6a5051c1922e1 NeedsCompilation: no Package: flowMerge Version: 2.55.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: 04b4264419548b5dc4f1522582913c5a NeedsCompilation: no Package: flowPeaks Version: 1.53.1 Depends: R (>= 2.12.0) Suggests: flowCore License: Artistic-1.0 MD5sum: 9b6e2f39586e3f3b86ee787b1c3cd79c NeedsCompilation: yes Package: flowPloidy Version: 1.33.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: 6af5ce927d0f25adbf60b75066a2a0b6 NeedsCompilation: no Package: flowPlots Version: 1.55.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: ab78689d9417b284d2f745a0c6034449 NeedsCompilation: no Package: FlowSOM Version: 2.15.0 Depends: R (>= 4.0), igraph Imports: stats, utils, colorRamps, ConsensusClusterPlus, dplyr, flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices, magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity License: GPL (>= 2) MD5sum: ae5fca973d7c296c74a4584bb3c6ccf1 NeedsCompilation: yes Package: flowSpecs Version: 1.21.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), BiocGenerics (>= 0.30.0), BiocParallel (>= 1.18.1), Biobase (>= 2.48.0), reshape2 (>= 1.4.3), flowCore (>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0) Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR License: MIT + file LICENSE MD5sum: e89e12aae367e03e3c36c9cc3c915c85 NeedsCompilation: no Package: flowStats Version: 4.19.0 Depends: R (>= 3.0.2) Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov, corpcor, mnormt, clue Suggests: xtable, testthat, openCyto, ggcyto, ggridges Enhances: RBGL,graph License: Artistic-2.0 MD5sum: 38e375e92a235038ab9ea6f5b20abeac NeedsCompilation: no Package: flowTime Version: 1.31.0 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto License: Artistic-2.0 MD5sum: 479db96b4a29d2fe0986cbf3e1bcd91b NeedsCompilation: no Package: flowTrans Version: 1.59.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 22ca6fd59a4043a981a23cb2654a9379 NeedsCompilation: no Package: flowViz Version: 1.71.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat License: Artistic-2.0 MD5sum: ab8abd5113b81f5b3fa613108d1aac8b NeedsCompilation: no Package: flowVS Version: 1.39.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 MD5sum: bf5414dd3af2812e81c55dc17431a53f NeedsCompilation: no Package: flowWorkspace Version: 4.19.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 2.13.1), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales(>= 1.3.0), matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto License_restricts_use: no MD5sum: 766c3c1d4af2ec58df4e8f0d10ffc61a NeedsCompilation: yes Package: fmcsR Version: 1.49.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown, codetools License: Artistic-2.0 MD5sum: 570a38181982605e9ce2d04bb7a15496 NeedsCompilation: yes Package: fmrs Version: 1.17.0 Depends: R (>= 4.3.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL-3 MD5sum: 44e030a991f8b261b65a9abd563ab28d NeedsCompilation: yes Package: fobitools Version: 1.15.0 Depends: R (>= 4.1) Imports: clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse License: GPL-3 MD5sum: d4ac1a7c15f0540e283ac4061b3fd9a2 NeedsCompilation: no Package: FRASER Version: 2.3.0 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: RcppArmadillo, Rcpp Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase License: MIT + file LICENSE MD5sum: c4af61b252d78b8febe1bb202fee9fb9 NeedsCompilation: yes Package: frenchFISH Version: 1.19.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 4b0aa958dc81d8afdb6942de979bf35c NeedsCompilation: no Package: FRGEpistasis Version: 1.43.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: e939af95744d1936771efd0b41c98493 NeedsCompilation: no Package: frma Version: 1.59.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: bd9965e9b5f1d422f4620cf2677a002d NeedsCompilation: no Package: frmaTools Version: 1.59.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 66320a23dca0b8dea82d0c62c9dc7783 NeedsCompilation: no Package: funOmics Version: 1.1.0 Depends: R (>= 4.4.0), NMF Imports: NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db, dplyr, stringr Suggests: knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment, SummarizedExperiment, airway License: MIT + file LICENSE MD5sum: 27e7da30ae165ca5272166bd8573f58d NeedsCompilation: no Package: funtooNorm Version: 1.31.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: f2ce3720f6da37be24985d0077aa07d9 NeedsCompilation: no Package: FuseSOM Version: 1.9.0 Depends: R (>= 4.2.0) Imports: psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: b3c0a643a6c5d34eb4134f0c04744a09 NeedsCompilation: yes Package: GA4GHclient Version: 1.31.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: cac55083f03f2e232bdb4215ce11baa6 NeedsCompilation: no Package: GA4GHshiny Version: 1.29.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 2ed68886abf2042d1c3692dc8aa81f2f NeedsCompilation: no Package: gaga Version: 2.53.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 5df9179b409dd05e473add3eba7afb0d NeedsCompilation: yes Package: gage Version: 2.57.0 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 93290fa7281f2064318a5f6d6b6ec35f NeedsCompilation: no Package: GAprediction Version: 1.33.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 918003f283068c5e67a7988827538a47 NeedsCompilation: no Package: garfield Version: 1.35.0 Suggests: knitr License: GPL-3 MD5sum: 8dc5320e1c3b24a97960d8339671429d NeedsCompilation: yes Package: GARS Version: 1.27.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 194a80609ef8afa4b82a532611438178 NeedsCompilation: no Package: GateFinder Version: 1.27.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 24fcd82c35d0c4d05fecdd7114163b3f NeedsCompilation: no Package: gatom Version: 1.5.0 Depends: R (>= 4.3.0) Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, GGally, grid, ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: fc6aedcba23e0bf7010f028ab4402810 NeedsCompilation: no Package: GBScleanR Version: 2.1.1 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 8cfad29276871ffe3a66dfc82e383b28 NeedsCompilation: yes Package: gcapc Version: 1.31.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: 5b0b88ac974944f87451269bbac643bf NeedsCompilation: no Package: gcatest Version: 2.7.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: a2d99c00c123b21999aba948039b5ef6 NeedsCompilation: no Package: gCrisprTools Version: 2.13.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: 63e6b3d7cfdcad01c1d7370b76ee3b8d NeedsCompilation: no Package: gcrma Version: 2.79.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: b9ec3e607db211efa9ff3efd57092a60 NeedsCompilation: yes Package: GDCRNATools Version: 1.27.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, prettydoc, rmarkdown License: Artistic-2.0 MD5sum: 329645369f7a6e679006263f8d98c63f NeedsCompilation: no Package: gDNAx Version: 1.5.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData License: Artistic-2.0 MD5sum: 39829b1ee3a75485c9ec4aecf97d2324 NeedsCompilation: no Package: gDRimport Version: 1.5.2 Depends: R (>= 4.2) Imports: assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx, data.table, futile.logger, gDRutils (>= 1.3.17), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx Suggests: BiocStyle, gDRtestData (>= 1.3.3), gDRstyle (>= 1.3.3), knitr, purrr, qs, testthat License: Artistic-2.0 MD5sum: c3f04cc02733771bf24d717e5f8f68fb NeedsCompilation: no Package: gDRstyle Version: 1.5.1 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cf279af02844745a4e6211f5e1b4895c NeedsCompilation: no Package: gDRutils Version: 1.5.2 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, scales, testthat, tools, yaml License: Artistic-2.0 MD5sum: 9697b60c86b470ff8db643588175c783 NeedsCompilation: no Package: GDSArray Version: 1.27.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: f2472b1c547290281b8a6a194cc8ca21 NeedsCompilation: no Package: gdsfmt Version: 1.43.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 6870cb1e23bde011417fe463e11331ee NeedsCompilation: yes Package: GeDi Version: 1.3.0 Depends: R (>= 4.4.0) Imports: GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, circlize Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 5cc01f63020533b4e6eccee1d88b7a2f NeedsCompilation: no Package: GEM Version: 1.33.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: f27b9a0b5fd77003d0af5e4943a957ae NeedsCompilation: no Package: gemini Version: 1.21.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 330252ffa777c92b6e0295d5d3df544a NeedsCompilation: no Package: gemma.R Version: 3.3.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny License: Apache License (>= 2) MD5sum: c86375579111b2bf5767268472222a66 NeedsCompilation: no Package: genArise Version: 1.83.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 453cbd6a5b9e5f1411844da5d3eb2bca NeedsCompilation: no Package: geneAttribution Version: 1.33.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: f1ea9e6c0bf1546579c01e0dfcdf3fa1 NeedsCompilation: no Package: GeneBreak Version: 1.37.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: ed08e1367fe12a67c536532cae31a8c1 NeedsCompilation: no Package: geneClassifiers Version: 1.31.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: b3f5b0f806bf0467c2240e66284e538c NeedsCompilation: no Package: GeneExpressionSignature Version: 1.53.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: adb44f8d0655c4d19e0c2163172313da NeedsCompilation: no Package: genefilter Version: 1.89.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: c0a7aa5a34dd32fd0e5fd88261c2d009 NeedsCompilation: yes Package: GeneGA Version: 1.57.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 4f83d6ab6ade79efb21d1570af95ec49 NeedsCompilation: no Package: GeneGeneInteR Version: 1.33.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: ce52e64c41a3fb0331b7e4338cd27081 NeedsCompilation: yes Package: GeneMeta Version: 1.79.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 533275774692525b0f6d8b69a0ea281e NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.49.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: edfd464618335f78360ca90e4c0064d9 NeedsCompilation: yes Package: GeneOverlap Version: 1.43.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 86d88b9f8468f7baff086509fac46253 NeedsCompilation: no Package: geneplast Version: 1.33.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 2bc0bf20bcc0c9ad776c9a12a041e52a NeedsCompilation: no Package: geneplotter Version: 1.85.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 5a71dc891376a76babff0a5497d96310 NeedsCompilation: no Package: geneRecommender Version: 1.79.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: ece1387300be55ebea823259bbdaffc7 NeedsCompilation: no Package: GeneRegionScan Version: 1.63.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 9e57cfac88df55e5aac12dde4186af4a NeedsCompilation: no Package: geneRxCluster Version: 1.43.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 95737029fb44b5c816de39f6de1660a0 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.51.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 62e4a9091a54608ce93ab740c6bb32b6 NeedsCompilation: yes Package: GENESIS Version: 2.37.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: dc45129f64991877763e2379f72474e7 NeedsCompilation: yes Package: GeneStructureTools Version: 1.27.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 2dc8927a7c3358f42c847d48cfedf8b6 NeedsCompilation: no Package: geNetClassifier Version: 1.47.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: dc1abac4f7ed1509a9d4bc0a62024e3b NeedsCompilation: no Package: GeneticsPed Version: 1.69.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: e6abe1c9f8c6713677b635d23d6ee3b8 NeedsCompilation: yes Package: GeneTonic Version: 3.1.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 784d4f235916f8df15adb070fb7cea71 NeedsCompilation: no Package: geneXtendeR Version: 1.33.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: 9626a7a4d239aa4c3dce8fd3864e7432 NeedsCompilation: yes Package: GENIE3 Version: 1.29.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: ba7b397291d20d31a10cabdf3aa7cf86 NeedsCompilation: yes Package: genoCN Version: 1.59.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: e45dd1bb1825e2484e2d676a26dcd3a1 NeedsCompilation: yes Package: genomation Version: 1.39.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: ddc73d57b46d70e9280b353d6d9c8fa5 NeedsCompilation: yes Package: GenomAutomorphism Version: 1.9.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 6375add4544342e94c2daa019db2719d NeedsCompilation: no Package: GenomeInfoDb Version: 1.43.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 3c291fb019be65136586611c99f46c88 NeedsCompilation: no Package: genomeIntervals Version: 1.63.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 77f0a207a62d086208aedf25d78d93b9 NeedsCompilation: no Package: genomes Version: 3.37.0 Depends: readr, curl License: GPL-3 MD5sum: dae05ba81e818f034fac20dbcec8f55e NeedsCompilation: no Package: GenomicAlignments Version: 1.43.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 2e03f7ccaecb69c76382bcac5d4e3849 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.31.0 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: 2614b49ae889fec0028d20c4d4318fa0 NeedsCompilation: no Package: GenomicDistributions Version: 1.15.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: a6a9291416dc08b35c7a31187da9240c NeedsCompilation: no Package: GenomicFeatures Version: 1.59.1 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 7b12f556e66b1cc86f47c3b8fba885f5 NeedsCompilation: no Package: GenomicFiles Version: 1.43.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: cfea074c49b3ec19fc7ed49c6fa11d48 NeedsCompilation: no Package: genomicInstability Version: 1.13.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: a36fa1245e429b6b8f227f21577537f0 NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.11.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 60a4a61ea60ad5e946cd41a7762a53f5 NeedsCompilation: no Package: GenomicInteractions Version: 1.41.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 72890628f2db2d7333bb6a9188d09fce NeedsCompilation: no Package: GenomicOZone Version: 1.21.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 9719f701ee02bb9fefad6e649f8d086c NeedsCompilation: no Package: GenomicPlot Version: 1.5.0 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, GenomeInfoDb, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi License: GPL-2 MD5sum: 36f7229efcc11b9c8ba7b588852373ef NeedsCompilation: no Package: GenomicRanges Version: 1.59.1 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), GenomeInfoDb (>= 1.43.1) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 15318a339da11d8cbaa476ae63137912 NeedsCompilation: yes Package: GenomicScores Version: 2.19.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: e1d4d64b94d1be0a1f950e2ceeeb6e31 NeedsCompilation: no Package: GenomicSuperSignature Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 6d24d51cac0fbd8a135e53044f02d556 NeedsCompilation: no Package: GenomicTuples Version: 1.41.1 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 MD5sum: 0a3008d71c7f4f003dead5a1a8aae444 NeedsCompilation: yes Package: GenProSeq Version: 1.11.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: b885a9b2d5d2edfe10e03c117825d698 NeedsCompilation: no Package: GenVisR Version: 1.39.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: 87f8f68a1e14b7c50d048ac388449224 NeedsCompilation: no Package: GeoDiff Version: 1.13.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: c38af61909fd4e14c12f89bf090acca6 NeedsCompilation: yes Package: GEOexplorer Version: 1.13.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: d958e826cb3f82d45016c524578a280e NeedsCompilation: no Package: GEOfastq Version: 1.15.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 44f73f06eeda9fba0e833cf40e82335c NeedsCompilation: no Package: geomeTriD Version: 1.1.1 Depends: R (>= 4.4.0) Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 58c3d7493478524ac14b39e28c6a522b NeedsCompilation: no Package: GeomxTools Version: 3.11.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: fee07998ac5baedd5b7d8afe3df55efe NeedsCompilation: no Package: GEOquery Version: 2.75.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT + file LICENSE MD5sum: c2fe537f5a4f392721ca06b02d72a3fb NeedsCompilation: no Package: GEOsubmission Version: 1.59.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 71681b7ff7748e885a7d2bf4526dca72 NeedsCompilation: no Package: GeoTcgaData Version: 2.7.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: 41861e6be3d1fb356ec3be8bacf916b8 NeedsCompilation: no Package: gep2pep Version: 1.27.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: b410ffe8297f221ea3c80ed9ccf1ac8d NeedsCompilation: no Package: getDEE2 Version: 1.17.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 6e156117bca4bed170f29df8df24c305 NeedsCompilation: no Package: geva Version: 1.15.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 94faaabc99a34bdbe92afda8d61f2b83 NeedsCompilation: no Package: GEWIST Version: 1.51.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: a5923199545cab4f38f2b32125172ec4 NeedsCompilation: no Package: gg4way Version: 1.5.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr License: MIT + file LICENSE MD5sum: f01db7c0264c1f61bb3ef2fe23fba14e NeedsCompilation: no Package: ggbio Version: 1.55.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 5bd9bce4f66ee9564c6071d78bde3303 NeedsCompilation: no Package: ggcyto Version: 1.35.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: e7bbdb05371ed796964828177de690fe NeedsCompilation: no Package: ggkegg Version: 1.5.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 84531c180ac0fbddcd484d47ec276ead NeedsCompilation: no Package: ggmanh Version: 1.11.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: 96897f0e2e4f5a8b4a9011a200a04030 NeedsCompilation: no Package: ggmsa Version: 1.13.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 08355d567645aaf4f48f4a00ed395610 NeedsCompilation: no Package: GGPA Version: 1.19.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: fb6053eb870f7dbd3e5a79709ab02d6c NeedsCompilation: yes Package: ggsc Version: 1.5.0 Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 1faa602e3dbcc94518b181cb5c3d35d0 NeedsCompilation: yes Package: ggseqalign Version: 1.1.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: f19bb91fcda69d877ee890e6b1e85a8c NeedsCompilation: no Package: ggspavis Version: 1.13.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 6a55a885cccd2399e9c02fdd8dc1ee02 NeedsCompilation: no Package: ggtree Version: 3.15.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: e6e370294b42f85c77689f426ea6caa6 NeedsCompilation: no Package: ggtreeDendro Version: 1.9.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: df5a67737c1d7da95c7a70710108023c NeedsCompilation: no Package: ggtreeExtra Version: 1.17.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: 52ec85f98a6658c924536ffefaffc7d0 NeedsCompilation: no Package: ggtreeSpace Version: 1.3.0 Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 07cb1d853ce0917e0e70df9beb38c82a NeedsCompilation: no Package: GIGSEA Version: 1.25.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 970533d0cc85ca2b6827c4147bf69dfd NeedsCompilation: no Package: ginmappeR Version: 1.3.1 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 33804952035f003d2b65819c7832906e NeedsCompilation: no Package: gINTomics Version: 1.3.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: f44ab279a1201e3e292d834875f95320 NeedsCompilation: no Package: girafe Version: 1.59.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), pwalign, graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: 8035a2033daf769697cb69dba29b6fb5 NeedsCompilation: yes Package: GLAD Version: 2.71.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 8f7b39144bdaad24d240809cb1dcb3ce NeedsCompilation: yes Package: GladiaTOX Version: 1.23.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 9fa799d4bc2d1ed96b918962bf1a374c NeedsCompilation: no Package: Glimma Version: 2.17.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran License: GPL-3 MD5sum: 16d7ab6e174541eb7dcf0098e5d621e1 NeedsCompilation: no Package: glmGamPoi Version: 1.19.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray (>= 1.5.21), DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr License: GPL-3 MD5sum: 0348e811e4486ab2b85abf4a0ff2f75d NeedsCompilation: yes Package: glmSparseNet Version: 1.25.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 MD5sum: 1674da34f781b5a36088759e54528683 NeedsCompilation: no Package: GlobalAncova Version: 4.25.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 95f934dc780d868a0edfa9a535b44cff NeedsCompilation: yes Package: globalSeq Version: 1.35.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 82503f8353883178ee5503ae12c8b245 NeedsCompilation: no Package: globaltest Version: 5.61.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: 1b16186bde528acc0ce0766249f8984f NeedsCompilation: no Package: GloScope Version: 1.5.0 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: 9fded23ee3a3e47a413f0632ca535a59 NeedsCompilation: no Package: gmapR Version: 1.49.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: b42d9c94e51a80c60b0aac79a8bf42f3 NeedsCompilation: yes Package: GmicR Version: 1.21.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 319ed322a3c55d2a74d8f64a59eba19c NeedsCompilation: no Package: gmoviz Version: 1.19.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: c4a8540b1a0fa3fd8183ebf07dd150a5 NeedsCompilation: no Package: GMRP Version: 1.35.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: b83e883e39526efa3aacdf3d25c6af25 NeedsCompilation: no Package: GNET2 Version: 1.23.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 75259c0f570ea6ae1e968f8fe552f392 NeedsCompilation: yes Package: GNOSIS Version: 1.5.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8122dc73fb552a75eccf80fb0d28b747 NeedsCompilation: no Package: GOexpress Version: 1.41.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: 3b17ab255807ac9aa93b5591162c1fd7 NeedsCompilation: no Package: GOfuncR Version: 1.27.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 4c14aa224d718feb0cb350454fd12723 NeedsCompilation: yes Package: GOpro Version: 1.33.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 4d5cb94a8683f861d5a3d43f1834ad58 NeedsCompilation: yes Package: goProfiles Version: 1.69.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 9ce163968fed115b0476a65dae740117 NeedsCompilation: no Package: GOSemSim Version: 2.33.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.1.6) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 413ad21f835b8b411ccf3cef1f8c7158 NeedsCompilation: yes Package: goseq Version: 1.59.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, GenomeInfoDb Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: dd8bb1ce8a3a2ad7b5d72b5b498a1249 NeedsCompilation: no Package: goSorensen Version: 1.9.0 Depends: R (>= 4.3) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 26d4c4e929aca5f1f4d36f78b1c9c434 NeedsCompilation: no Package: goSTAG Version: 1.31.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a07925ede5f939382476258e53ad1444 NeedsCompilation: no Package: GOstats Version: 2.73.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 615bb6e4c02a678912df97e8d9a43d92 NeedsCompilation: no Package: GOTHiC Version: 1.43.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: c9f44f8f6298ef87708580cab72baea1 NeedsCompilation: no Package: goTools Version: 1.81.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 3caefa49b01ca79d0242a4e9cdce7533 NeedsCompilation: no Package: GPA Version: 1.19.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: 5580d226b5700c1a5955c7f67b9f1617 NeedsCompilation: yes Package: gpls Version: 1.79.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 0d7fd8d90ec0d098e47a44f74d32750d NeedsCompilation: no Package: gpuMagic Version: 1.23.0 Depends: R (>= 3.6.0), methods, utils Imports: Deriv, DescTools, digest, pryr, stringr, BiocGenerics LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2406c611a2c17a7834959ed57aea298f NeedsCompilation: yes Package: GrafGen Version: 1.3.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, zlibbioc, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 2a4cb7a3d73f1589c211e73f8dd97278 NeedsCompilation: yes Package: GRaNIE Version: 1.11.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 MD5sum: ecde9ce0b2c0fe073791d85cd8ff06dd NeedsCompilation: no Package: granulator Version: 1.15.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8280e2deaba8dd3a239cdb08b6e3e3b3 NeedsCompilation: no Package: graper Version: 1.23.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: e141f1412fcae49e4dcdaa67872f5349 NeedsCompilation: yes Package: graph Version: 1.85.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: 211b8dec75acffc640bd68864f58b739 NeedsCompilation: yes Package: GraphAlignment Version: 1.71.0 License: file LICENSE License_restricts_use: yes MD5sum: 9f0915a96c528eb4186f11b2a0235aeb NeedsCompilation: yes Package: GraphAT Version: 1.79.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: d5d435e9756b6b39c7375563fa535290 NeedsCompilation: no Package: graphite Version: 1.53.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 3cc81f42b9b9fcedb30731b9bd3a8c01 NeedsCompilation: no Package: GRENITS Version: 1.59.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: a6c0acb85a8e5bd4fd86ee5c593eed48 NeedsCompilation: yes Package: GreyListChIP Version: 1.39.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 59d1f6e897dc1fad22568790039a7726 NeedsCompilation: no Package: GRmetrics Version: 1.33.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: 5475419908cb6438495231ab376f2c06 NeedsCompilation: no Package: GSALightning Version: 1.35.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 0119a7f58c43b4863dce710c42126208 NeedsCompilation: no Package: GSAR Version: 1.41.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 4d989333329a423a1ea3de72a0748942 NeedsCompilation: no Package: GSCA Version: 2.37.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 638626be275c7ce865b2c384608d6a37 NeedsCompilation: no Package: gscreend Version: 1.21.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 840e3d21b837d7a97c068ea2fa2ccd61 NeedsCompilation: no Package: GSEABase Version: 1.69.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: da00e58239d65a1a25122685963540d2 NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.27.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: 8d4bbd34303acf44f0614054cdd1aa23 NeedsCompilation: no Package: GSEAlm Version: 1.67.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 2486c505d9f23474c702e814cef676cf NeedsCompilation: no Package: GSEAmining Version: 1.17.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: 687e214c785f18de67516123de3206ea NeedsCompilation: no Package: gsean Version: 1.27.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: e04286a690b56f7042c21ae4c08c183d NeedsCompilation: yes Package: GSgalgoR Version: 1.17.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 32f43d5754160bf6fb5b6352e92a314c NeedsCompilation: no Package: GSReg Version: 1.41.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: f29c09b7f03d4bda2b4e1eff2ac7a0a3 NeedsCompilation: yes Package: GSRI Version: 2.55.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: d0c5140cb37bdbfa082741f95884dd5a NeedsCompilation: no Package: GSVA Version: 2.1.1 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular, cli LinkingTo: cli Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: bae03279c82d0250c057366b3991d946 NeedsCompilation: yes Package: gtrellis Version: 1.39.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: b9045b6bb4acfbed12419baa8768681d NeedsCompilation: no Package: GUIDEseq Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 7ea8ae85c95700b0244a6bdc547235d6 NeedsCompilation: no Package: Guitar Version: 2.23.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 8885c8ad55a7639303addac39369712e NeedsCompilation: no Package: Gviz Version: 1.51.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 7d5393d2029b0e09f2ad52adb60abc4e NeedsCompilation: no Package: GWAS.BAYES Version: 1.17.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 8240beed7ffee9b583e661db57e4b2c1 NeedsCompilation: no Package: gwascat Version: 2.39.0 Depends: R (>= 3.5.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: 15f505e9dc87b627305eb2214c09a938 NeedsCompilation: no Package: GWASTools Version: 1.53.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 35e335f32b53b5ead5085039a768010a NeedsCompilation: no Package: gwasurvivr Version: 1.25.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1d5f28130207c5065e692cc7545e2201 NeedsCompilation: no Package: GWENA Version: 1.17.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: 9b214ac4abefdd1b5bd7f7223358d60b NeedsCompilation: no Package: gypsum Version: 1.3.0 Imports: utils, httr2, jsonlite, parallel, filelock, rappdirs Suggests: knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate, DBI, RSQLite, S4Vectors, methods License: MIT + file LICENSE MD5sum: e21eed74adb2850fa6a06ec9576a9ed9 NeedsCompilation: no Package: h5vc Version: 2.41.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.99.1) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) MD5sum: d88661a6b6fe40b63aea1890cb2a449d NeedsCompilation: yes Package: hapFabia Version: 1.49.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 43558a996af670e27850187db87c8b5f NeedsCompilation: yes Package: Harman Version: 1.35.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: a70de6b8a59093b02e4b45f06cec0369 NeedsCompilation: yes Package: HarmonizR Version: 1.5.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma (>= 3.46.0), SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 9bd022c25b3fd617ca6d04246cd2603d NeedsCompilation: no Package: Harshlight Version: 1.79.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: 6ef2f45f8f9ccedcff290c7641f37f9c NeedsCompilation: yes Package: hca Version: 1.15.0 Depends: R (>= 4.1) Imports: httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache, tools, utils, digest, shiny, miniUI, DT Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 2def23df0224ef4f6685746b5c0f1b3e NeedsCompilation: no Package: HDF5Array Version: 1.35.1 Depends: R (>= 3.4), methods, SparseArray (>= 1.5.42), DelayedArray (>= 0.33.1), rhdf5 (>= 2.31.6) Imports: utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>= 0.51.2), S4Vectors, IRanges, S4Arrays (>= 1.1.1) LinkingTo: S4Vectors (>= 0.27.13), Rhdf5lib Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter License: Artistic-2.0 MD5sum: 9012c80bf995057382fe6276897e0b1f NeedsCompilation: yes Package: HDTD Version: 1.41.0 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 217f915f9f0d33aa9042cae66100d4dd NeedsCompilation: yes Package: hdxmsqc Version: 1.3.0 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE MD5sum: d3435039c6516e3674560cebe524fc18 NeedsCompilation: no Package: heatmaps Version: 1.31.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 64872a90e60068f12c49744a64153dfc NeedsCompilation: no Package: Heatplus Version: 3.15.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: d63b8115d5202e58f7c7d0d74c96ec0e NeedsCompilation: no Package: HelloRanges Version: 1.33.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment, BiocIO Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 0505cfd72189a08447387c4f2344edef NeedsCompilation: no Package: HELP Version: 1.65.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: d6ac978c90b9ccda8940d9083b42c8d5 NeedsCompilation: no Package: HEM Version: 1.79.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: c2dca411ab25432c54b3b57d5d3c26c3 NeedsCompilation: yes Package: hermes Version: 1.11.0 Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16) Imports: assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>= 2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats, forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, S4Vectors, stats, tidyr, utils Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr License: Apache License 2.0 MD5sum: c8f8b92195ef5810566a0ae77a0d3237 NeedsCompilation: no Package: HERON Version: 1.5.0 Depends: R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges, IRanges, S4Vectors Imports: matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: ae204cb642f6466762c668d62efd237c NeedsCompilation: no Package: Herper Version: 1.17.0 Depends: R (>= 4.0), reticulate Imports: utils, rjson, withr, stats Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 02eff3bb7ec941338edb44b7643560f1 NeedsCompilation: no Package: HGC Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: be69dfb4c0e1d29aae8a203a3be549f5 NeedsCompilation: yes Package: hiAnnotator Version: 1.41.0 Depends: GenomicRanges, R (>= 2.10) Imports: foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods Suggests: knitr, doParallel, testthat, BiocGenerics, markdown License: GPL (>= 2) MD5sum: f4c84ccc8e20355a1d22040fc9b47650 NeedsCompilation: no Package: HIBAG Version: 1.43.1 Depends: R (>= 3.2.0) Imports: methods, RcppParallel LinkingTo: RcppParallel (>= 5.0.0) Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools License: GPL-3 MD5sum: 7bab737223a3cced04a11debeb95d0ed NeedsCompilation: yes Package: HicAggR Version: 1.3.0 Depends: R (>= 4.2.0) Imports: InteractionSet, BiocGenerics, BiocParallel, dplyr, GenomeInfoDb, GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods, rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr, tibble, stringr, tidyr, gridExtra, data.table, reshape, checkmate, purrr, withr Suggests: covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) License: MIT + file LICENSE MD5sum: c7aff2e8cc6294b28fdb05f649e4835a NeedsCompilation: no Package: HiCBricks Version: 1.25.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b60ff97b743516c921e2951ac87b5649 NeedsCompilation: no Package: HiCcompare Version: 1.29.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: e0630fb56464ecd9ca04fdbfc2d2fd76 NeedsCompilation: no Package: HiCDCPlus Version: 1.15.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: 2003eaa7ca546056ee12e1723c122f44 NeedsCompilation: yes Package: HiCDOC Version: 1.9.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: b373e846cfa89b1573d3efe9b338b457 NeedsCompilation: yes Package: HiCExperiment Version: 1.7.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 87df9494d039ac01483da24ef8045797 NeedsCompilation: no Package: HiContacts Version: 1.9.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0b1df6d0a448ae54d63d9f6f767279e2 NeedsCompilation: no Package: HiCool Version: 1.7.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 80bbd38dd71838be0a0a254b04160170 NeedsCompilation: no Package: hicVennDiagram Version: 1.5.0 Depends: R (>= 4.3.0) Imports: GenomeInfoDb, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene License: GPL-3 MD5sum: 14c2cd47d3a3cf813f37e7d12b34cdce NeedsCompilation: no Package: hierGWAS Version: 1.37.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: f34e1edb03571790caa113a908f2ec28 NeedsCompilation: no Package: hierinf Version: 1.25.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: b698b6f920b3cc2e9d23e8df219e1dff NeedsCompilation: no Package: HilbertCurve Version: 2.1.0 Depends: R (>= 4.0.0), grid Imports: methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr, Rcpp LinkingTo: Rcpp Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE MD5sum: f74cd989521a322b403c568cf4c9caed NeedsCompilation: yes Package: HilbertVis Version: 1.65.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: 344126afb55ca55662be7c7d40c14ab7 NeedsCompilation: yes Package: HilbertVisGUI Version: 1.65.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) MD5sum: 20533513836de7a80b49aefaa62c01e8 NeedsCompilation: yes Package: HiLDA Version: 1.21.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: df84f2f52c9d85330421b431794f29e1 NeedsCompilation: yes Package: hipathia Version: 3.7.0 Depends: R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors, ggplot2, ggpubr, dplyr, tibble, visNetwork, reshape2, MetBrewer Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 07d352e397f623fe73e6a6c7e4f2951d NeedsCompilation: no Package: HIPPO Version: 1.19.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 0e70e9fd11abdc4e3828e969e64c2a69 NeedsCompilation: no Package: hiReadsProcessor Version: 1.43.0 Depends: R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments, BiocParallel, hiAnnotator Imports: sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods Suggests: knitr, testthat, markdown License: GPL-3 MD5sum: b80d2d7b95e06d07082c8b9f448a340c NeedsCompilation: no Package: HIREewas Version: 1.25.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: 4aabd8e5e4fb80bd69508c2a7faac4c5 NeedsCompilation: yes Package: HiTC Version: 1.51.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, GenomeInfoDb Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 MD5sum: a1ca38bd3c9534d76f952528e4dec185 NeedsCompilation: no Package: hmdbQuery Version: 1.27.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 MD5sum: 79a222938f6a8b2587d58a0f7c6df2be NeedsCompilation: no Package: HMMcopy Version: 1.49.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 MD5sum: 1e18b2621b069075ea77d334344211c0 NeedsCompilation: yes Package: HoloFoodR Version: 1.1.0 Depends: R(>= 4.4.0), TreeSummarizedExperiment, MultiAssayExperiment Imports: dplyr, httr2, jsonlite, S4Vectors, stats, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 097d6c3d4fbc03d2782c6a5f5d0eb8a4 NeedsCompilation: no Package: hoodscanR Version: 1.5.0 Depends: R (>= 4.3) Imports: knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: c51c4d7f3c3c790ce0cfe1222febc4f5 NeedsCompilation: yes Package: hopach Version: 2.67.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: 55279eba3e6c6e7b9819a5dbd7926105 NeedsCompilation: yes Package: HPAanalyze Version: 1.25.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 2876647d9806621ec1e5b0f030a9c921 NeedsCompilation: no Package: hpar Version: 1.49.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: a36c8779696ea3bc0b5ee98c3cc39cc6 NeedsCompilation: no Package: HPiP Version: 1.13.0 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: 6b72504483f6b537a67f4f2373feefd2 NeedsCompilation: no Package: HTSFilter Version: 1.47.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0500aad07d4ed2ec5fc62eaa4341fca3 NeedsCompilation: no Package: HuBMAPR Version: 1.1.4 Depends: R (>= 4.4.0) Imports: httr2, dplyr, tidyr, tibble, rjsoncons, rlang, utils, stringr, whisker, purrr Suggests: testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 7297e1500f7242ad25e8594d930568d8 NeedsCompilation: no Package: HubPub Version: 1.15.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 MD5sum: a3b2193393df55ccb8e912ca16a35b80 NeedsCompilation: no Package: hummingbird Version: 1.17.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 3f1a24c568f16a0400df56ce42ba123b NeedsCompilation: yes Package: HybridExpress Version: 1.3.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 10597b654d2f90371966642513caec12 NeedsCompilation: no Package: HybridMTest Version: 1.51.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: 5d39e4e60a51d08bd4d258c9c985f504 NeedsCompilation: no Package: hypeR Version: 2.5.0 Depends: R (>= 3.6.0) Imports: ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny, BiocStyle Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 9dc7205d966b3e13d0125b904fd54253 NeedsCompilation: no Package: hyperdraw Version: 1.59.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: e0d43591b53642a3702a9378e10bd2fe NeedsCompilation: no Package: hypergraph Version: 1.79.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 MD5sum: ee7fd25509e00cb6d04ba93fd9f4b220 NeedsCompilation: no Package: iASeq Version: 1.51.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: 983607606a0d80f499f84f43d72e6a92 NeedsCompilation: no Package: iasva Version: 1.25.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 MD5sum: 9b3019881850ade3b2193b62c2552e73 NeedsCompilation: no Package: iBBiG Version: 1.51.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: 0905aee1dcd57fe89f9283c868b10e79 NeedsCompilation: yes Package: ibh Version: 1.55.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: 3a81381c6440acf97eadf13924a4aed4 NeedsCompilation: no Package: iBMQ Version: 1.47.0 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 MD5sum: a545e1d14e55fa3853dff76aa871b347 NeedsCompilation: yes Package: iCARE Version: 1.35.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE MD5sum: 0e9725db4a47d7c5fefb5677c55b6266 NeedsCompilation: yes Package: Icens Version: 1.79.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: b83efacf90773a1b038a5cee3524cfdd NeedsCompilation: no Package: icetea Version: 1.25.0 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 7817515f9ddaf10ead9fb7ca79cddb78 NeedsCompilation: no Package: iCheck Version: 1.37.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: b0e307c80db1be2d39dcad2d96c8221c NeedsCompilation: no Package: iChip Version: 1.61.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 602222977534c27e9e2f41cbc8cb2853 NeedsCompilation: yes Package: iClusterPlus Version: 1.43.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: f746687eaf532e8e6b91639fa7f246fc NeedsCompilation: yes Package: iCNV Version: 1.27.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: b18c0c5d596240fb921148bfb6a0cf5f NeedsCompilation: no Package: iCOBRA Version: 1.35.0 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, markdown, utils, rlang Suggests: knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: a0b7b797a78e8384ed3ad67af75359ce NeedsCompilation: no Package: ideal Version: 2.1.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, graphics, base64enc, methods, utils, stats Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR License: MIT + file LICENSE MD5sum: e6e59d70f4466caf40564d8bb8192a62 NeedsCompilation: no Package: IdeoViz Version: 1.43.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: a1c336c595cdf718138ed8ee5ea0265d NeedsCompilation: no Package: idiogram Version: 1.83.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: ea355153a09177abbc5c02212cd0ca46 NeedsCompilation: no Package: idpr Version: 1.17.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: 631de9c69b10fafc0cacbe655cc451a1 NeedsCompilation: no Package: idr2d Version: 1.21.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1), grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 488ed81955108ab84b743ce346960849 NeedsCompilation: no Package: IFAA Version: 1.9.0 Depends: R (>= 4.2.0), Imports: mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11), parallelly , glmnet, stats, utils, SummarizedExperiment, stringr, S4Vectors, DescTools, MatrixExtra, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: bdf772320600f2cad0e79b084be9d9c9 NeedsCompilation: no Package: iGC Version: 1.37.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: 02a13bebc0c5ff6d64c10304cd96b2d6 NeedsCompilation: no Package: IgGeneUsage Version: 1.21.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE MD5sum: eabf6a2295c976be0bce0973e18b99fe NeedsCompilation: yes Package: igvR Version: 1.27.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: 2b627e18c27e4966e97c358d1919b115 NeedsCompilation: no Package: igvShiny Version: 1.3.0 Depends: R (>= 3.5.0), GenomicRanges, methods, shiny Imports: BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, utils Suggests: BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, RUnit, shinytest2, VariantAnnotation License: MIT + file LICENSE MD5sum: 59482c9300e3063e708675e921b0e7b2 NeedsCompilation: no Package: IHW Version: 1.35.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 057a314663cb054ed6a6bc49ffe59f4c NeedsCompilation: no Package: illuminaio Version: 0.49.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: 4fc6b066a9ab10c6d1250aaecbee2bba NeedsCompilation: yes Package: ILoReg Version: 1.17.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 222c77945ffae592bc514f9d41f64e8e NeedsCompilation: no Package: IMAS Version: 1.31.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 MD5sum: befcd5c3a470d97ab382e5e75823553a NeedsCompilation: no Package: imcRtools Version: 1.13.0 Depends: R (>= 4.1), SpatialExperiment Imports: S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: ec87981b33f4860013871cea3d6eee7f NeedsCompilation: no Package: IMMAN Version: 1.27.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9e11c73ae21aa245f81bfbdfe39c15ed NeedsCompilation: no Package: immunoClust Version: 1.39.0 Depends: R(>= 3.6), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 MD5sum: 5da19971f6adebcb6b7cb16b1be8cd93 NeedsCompilation: yes Package: immunogenViewer Version: 1.1.0 Depends: R (>= 4.0) Imports: ggplot2, httr, jsonlite, patchwork, UniProt.ws Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT License: Apache License (>= 2) MD5sum: 7623f596eb29430dc0b81622aaa669a0 NeedsCompilation: no Package: immunotation Version: 1.15.0 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 MD5sum: 7761beb3d3f07f2747930b2cf3717e78 NeedsCompilation: no Package: IMPCdata Version: 1.43.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: 9f67c6aaef588f549f4c176f254b8088 NeedsCompilation: no Package: impute Version: 1.81.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 6c0c74800705cf0a04f7500770f571c4 NeedsCompilation: yes Package: INDEED Version: 2.21.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: 1682548f1f12fb64757be840192ecd6b NeedsCompilation: no Package: iNETgrate Version: 1.5.0 Depends: R (>= 4.3.0), BiocStyle (>= 2.18.1) Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA, grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26), Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast, tidyr, tidyselect, utils Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) License: GPL-3 MD5sum: 7fa52af0838f5006b9d03b80bd11c75e NeedsCompilation: no Package: infercnv Version: 1.23.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: df24c96b78e40c1ead33e83fe98a65d6 NeedsCompilation: no Package: infinityFlow Version: 1.17.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: 0d8e8d1de4ce1552077863bf0d149d0e NeedsCompilation: no Package: Informeasure Version: 1.17.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 184a35c135751226cec3341714e599bb NeedsCompilation: no Package: InPAS Version: 2.15.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr,methods,parallelly, plyranges, preprocessCore, readr,reshape2, RSQLite, stats,S4Vectors, utils Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) MD5sum: cc08d946814dee2343d75829e510f0ef NeedsCompilation: no Package: INPower Version: 1.43.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: b2f4eff27b4ae59e30ae717033d44855 NeedsCompilation: no Package: INSPEcT Version: 1.37.0 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 3beb5f79b402e70a485ee2a59d46b376 NeedsCompilation: no Package: INTACT Version: 1.7.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2 Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 59928e5db440a961a83ee923b038a4e2 NeedsCompilation: no Package: InTAD Version: 1.27.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 8f7867dcde0a211838cbb540d217dba0 NeedsCompilation: no Package: intansv Version: 1.47.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: d427bf514a9afc046119b89042930038 NeedsCompilation: no Package: interacCircos Version: 1.17.0 Depends: R (>= 4.1) Imports: RColorBrewer, htmlwidgets, plyr, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 2dfa499eaccdf6ee4d62fc3e4e83db72 NeedsCompilation: no Package: InteractionSet Version: 1.35.0 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, GenomeInfoDb LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 64888b2e7bb30e1b4f22a5d6ae664eea NeedsCompilation: yes Package: InteractiveComplexHeatmap Version: 1.15.0 Depends: R (>= 4.0.0), ComplexHeatmap (>= 2.11.0) Imports: grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite, RColorBrewer, fontawesome Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: 61cd9b90186c941db580101bb03093d8 NeedsCompilation: no Package: interactiveDisplayBase Version: 1.45.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 0013248584852a215739490f3432a998 NeedsCompilation: no Package: InterCellar Version: 2.13.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: d1b9955aa5cf68a7918d4e0c98fc98b5 NeedsCompilation: no Package: IntramiRExploreR Version: 1.29.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: fac728779bc94f8f14de8e647d0a6ca9 NeedsCompilation: no Package: IONiseR Version: 2.31.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: c30f2f6420db22002e52c8f8693f4c47 NeedsCompilation: no Package: iPath Version: 1.13.0 Depends: R (>= 4.1), mclust, BiocParallel, survival Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats LinkingTo: Rcpp, RcppArmadillo Suggests: rmarkdown, BiocStyle, knitr License: GPL-2 MD5sum: f48067f9f3bb44ccbf7156c60d61d205 NeedsCompilation: yes Package: ipdDb Version: 1.25.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 946179ec16dd2e6f25e63a45b078c3c9 NeedsCompilation: no Package: IPO Version: 1.33.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils Imports: BiocParallel Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr Enhances: parallel License: GPL (>= 2) + file LICENSE MD5sum: c0744f28c11a64976a9d8e3823430abb NeedsCompilation: no Package: IRanges Version: 2.41.1 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: a8d9796ee6d575ebd51f68053a44782a NeedsCompilation: yes Package: iSEE Version: 2.19.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: 9ac7f1bc4173be358928401dc7344b9f NeedsCompilation: no Package: iSEEde Version: 1.5.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 66cee6294aaafe1527e971b0c9232239 NeedsCompilation: no Package: iSEEfier Version: 1.3.0 Imports: iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 55dbead1277f722f21985e5a08459c95 NeedsCompilation: no Package: iSEEhex Version: 1.9.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 MD5sum: 4b3c07bbe65dd5c8e15f35fb1731b025 NeedsCompilation: no Package: iSEEhub Version: 1.9.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: c461ac4a2973209e404ef88a386011a3 NeedsCompilation: no Package: iSEEindex Version: 1.5.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown, scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: e70a6d368fc3018695a5187490867821 NeedsCompilation: no Package: iSEEpathways Version: 1.5.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 018a57ab767784c0d002743f4d50cb3b NeedsCompilation: no Package: iSEEtree Version: 1.1.0 Depends: R (>= 4.4.0), iSEE Imports: grDevices, methods, miaViz, S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils Suggests: biomformat, BiocStyle, knitr, MGnifyR, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan License: Artistic-2.0 MD5sum: 1b828ca46a117ab576d106aa8f5e98db NeedsCompilation: no Package: iSEEu Version: 1.19.0 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE MD5sum: d25d71ac493e83b19077ba094cda55fc NeedsCompilation: no Package: iSeq Version: 1.59.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 6382a55c713215430267e85be3d118ed NeedsCompilation: yes Package: ISLET Version: 1.9.0 Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls Imports: stats, methods, purrr, abind Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr License: GPL-2 MD5sum: 24951acce6e5ca7450f04378f8cdeea7 NeedsCompilation: no Package: isobar Version: 1.53.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 189dac6af3815bd6ff377963ad60aaa1 NeedsCompilation: no Package: IsoBayes Version: 1.5.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2, HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: fad672779e9b38732bba0f108eafd75d NeedsCompilation: yes Package: IsoCorrectoR Version: 1.25.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: b29c72535e281d6f39e3950f3bcd9b9b NeedsCompilation: no Package: IsoCorrectoRGUI Version: 1.23.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: fb9907a431025b25bf919c456e446e31 NeedsCompilation: no Package: ISoLDE Version: 1.35.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: fe15a189ea6f2fe0cfe1c3b9b6c02d28 NeedsCompilation: yes Package: isomiRs Version: 1.35.0 Depends: R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: ef3a3f886ccd5842943be4027c7159db NeedsCompilation: no Package: ITALICS Version: 2.67.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: 6da1e72b9ee3fcdb12b552fb277de3d6 NeedsCompilation: no Package: iterativeBMA Version: 1.65.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: a31b53ffecaf3451650f55a271457504 NeedsCompilation: no Package: iterativeBMAsurv Version: 1.65.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: 5f0db4b43ab1c2fdf2f85c00aeb29c18 NeedsCompilation: no Package: IVAS Version: 2.27.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: 7bdba9a5c95195792cc83e29fa991473 NeedsCompilation: no Package: ivygapSE Version: 1.29.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools License: Artistic-2.0 MD5sum: 4800b899c10d80f3c5458d2962c9965c NeedsCompilation: no Package: IWTomics Version: 1.31.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: 54809a6925fc13ab8ec1a2ff26aef68c NeedsCompilation: no Package: karyoploteR Version: 1.33.0 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: 575febb46f71f107e192ad9f57350d52 NeedsCompilation: no Package: katdetectr Version: 1.9.0 Depends: R (>= 4.2) Imports: Biobase (>= 2.54.0), BiocParallel (>= 1.26.2), BSgenome (>= 1.62.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4), changepoint (>= 2.2.3), changepoint.np (>= 1.0.3), checkmate (>= 2.0.0), dplyr (>= 1.0.8), GenomeInfoDb (>= 1.28.4), GenomicRanges (>= 1.44.0), ggplot2 (>= 3.3.5), ggtext (>= 0.1.1), IRanges (>= 2.26.0), maftools (>= 2.10.5), methods (>= 4.1.3), plyranges (>= 1.17.0), Rdpack (>= 2.3.1), rlang (>= 1.0.2), S4Vectors (>= 0.30.2), scales (>= 1.2.0), tibble (>= 3.1.6), tidyr (>= 1.2.0), tools, utils, VariantAnnotation (>= 1.38.0) Suggests: BiocStyle (>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: a55f0455612abd5b40ddd5f7d3f9cde3 NeedsCompilation: no Package: KBoost Version: 1.15.0 Depends: R (>= 4.1), stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 | GPL-3 MD5sum: 0c664c8502b9f68eca6628199ef0302a NeedsCompilation: no Package: KCsmart Version: 2.65.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: 5d4d18f1af1f0c74a494e7c04a161fae NeedsCompilation: no Package: kebabs Version: 1.41.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 759859e1abad227e8c1b9976e4e1ef74 NeedsCompilation: yes Package: KEGGgraph Version: 1.67.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: 93ace09026b443db8cb39ae4d8e280b8 NeedsCompilation: no Package: KEGGlincs Version: 1.33.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: b529e8ac2b959d99c697318472f4513a NeedsCompilation: no Package: keggorthology Version: 2.59.0 Depends: R (>= 2.5.0), hgu95av2.db, graph Imports: AnnotationDbi, DBI, grDevices, methods, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: d22e505ac9ef77b13947307b04ca5e22 NeedsCompilation: no Package: KEGGREST Version: 1.47.0 Depends: R (>= 3.5.0) Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 81419475dde18ef4164e7c26f9d23262 NeedsCompilation: no Package: KinSwingR Version: 1.25.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 8e706ae61faad1d3f42a9777dd39244f NeedsCompilation: no Package: kissDE Version: 1.27.0 Imports: aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT Suggests: BiocStyle, testthat License: GPL (>= 2) MD5sum: 700c37ebc0b227bb3e757b76696c792e NeedsCompilation: no Package: kmcut Version: 1.1.0 Imports: survival, tools, methods, pracma, doParallel, foreach, parallel, SummarizedExperiment, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, License: Artistic-2.0 MD5sum: 8ea024181c4482d2390c5afb5c3a444e NeedsCompilation: no Package: KnowSeq Version: 1.21.0 Depends: R (>= 4.0), cqn (>= 1.28.1) Imports: stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab, rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML, praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3), limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: 8ec747eefa20aef52a39f0aabd31d784 NeedsCompilation: no Package: knowYourCG Version: 1.3.0 Depends: R (>= 4.4.0) Imports: sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2 License: MIT + file LICENSE MD5sum: 1503ea493cd131febe41a703954a9bd4 NeedsCompilation: no Package: koinar Version: 1.1.0 Depends: R (>= 4.3) Imports: httr, jsonlite, methods, utils Suggests: BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice, msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat, mzR License: Apache License 2.0 MD5sum: 8cb21ec146e8114f9edb0dba6961ad1f NeedsCompilation: no Package: LACE Version: 2.11.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 877b352a6390e98aeb4cc998340f3dd4 NeedsCompilation: no Package: LBE Version: 1.75.0 Depends: stats Imports: graphics, stats, utils Suggests: qvalue License: GPL-2 MD5sum: e6cb772c9dee7d4cc767b52139dc5f2a NeedsCompilation: no Package: ldblock Version: 1.37.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: 8cf0d38bbf6d8891bad058896297f2ca NeedsCompilation: no Package: LEA Version: 3.19.1 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: 636d9b698d3d398f77a93249b44d74f8 NeedsCompilation: yes Package: LedPred Version: 1.41.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: 85f140e27d3223e7392b8cc324e33c98 NeedsCompilation: no Package: lefser Version: 1.17.1 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr License: Artistic-2.0 MD5sum: 75166fe88268d445c0235cefb4cc4861 NeedsCompilation: no Package: lemur Version: 1.5.0 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0), glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 5dcc004463111d8c134e2bb79c2e2465 NeedsCompilation: yes Package: les Version: 1.57.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 6a64fbc99dd458a4ffd328adc5b5bb19 NeedsCompilation: no Package: levi Version: 1.25.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 789edb284541cc686c1e617d3e17e1c2 NeedsCompilation: yes Package: lfa Version: 2.7.0 Depends: R (>= 4.0) Imports: utils, methods, corpcor, RSpectra Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: bc372f60a806789e8ad9d370a00f2eaa NeedsCompilation: yes Package: limma Version: 3.63.2 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) MD5sum: dc4562775761127ee367f5ddc9e00c59 NeedsCompilation: yes Package: limmaGUI Version: 1.83.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: d52b811ebb3b4565ecb47d7c79b387d7 NeedsCompilation: no Package: limpca Version: 1.3.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 89a075372214446c17a8c5368826f71d NeedsCompilation: no Package: lineagespot Version: 1.11.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 42c31ddd6813956bc966b40280df08d9 NeedsCompilation: no Package: LinkHD Version: 1.21.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: e4a3547ac5521befec0bdaf0db8288d4 NeedsCompilation: no Package: Linnorm Version: 2.31.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE MD5sum: 24193fd4aef073ee40073d0b40b6f515 NeedsCompilation: yes Package: LinTInd Version: 1.11.0 Depends: R (>= 4.0), ggplot2, parallel, stats, S4Vectors Imports: data.tree, reshape2, networkD3, stringdist, purrr, ape, cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap, Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: ae20498a4e1bee1d7f6a7f71e7e0159e NeedsCompilation: no Package: lionessR Version: 1.21.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: 9ff331891af088bca45c13ffb94715fb NeedsCompilation: no Package: lipidr Version: 2.21.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 9caab0a213c881642f9881b0db1148e3 NeedsCompilation: no Package: LiquidAssociation Version: 1.61.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 31ae064cfd3b7fe7b81c7cdb6c1ec44b NeedsCompilation: no Package: lisaClust Version: 1.15.6 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random, lifecycle, simpleSeg, rlang, Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 5d179b9a2588b550af1ba82492671969 NeedsCompilation: no Package: lmdme Version: 1.49.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 44aac4b2d23bd9bbc6c1515c6d011fa1 NeedsCompilation: no Package: LOBSTAHS Version: 1.33.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: fd54d0828739d76f7b1932d52ac57282 NeedsCompilation: no Package: loci2path Version: 1.27.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e0dae695c17ecda22c76323f2b3f8c8a NeedsCompilation: no Package: logicFS Version: 2.27.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: 7623c570de1e33c11c74c9352947d5b0 NeedsCompilation: no Package: LOLA Version: 1.37.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: 363de05d168ba6d92a1b8a609fbb6a05 NeedsCompilation: no Package: LoomExperiment Version: 1.25.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: ba633778f94d20f7cfc04c6fde6dd70d NeedsCompilation: no Package: LPE Version: 1.81.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: 5b7b5b701904d47f44302eef1b30a295 NeedsCompilation: no Package: lpNet Version: 2.39.0 Depends: lpSolve, KEGGgraph License: Artistic License 2.0 MD5sum: f9819edb87c43ea5d390033b60269c6b NeedsCompilation: no Package: lpsymphony Version: 1.35.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL MD5sum: e893d4b6265274a8dad484928a11dcfc NeedsCompilation: yes Package: LRBaseDbi Version: 2.17.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: testthat, BiocStyle, AnnotationHub License: Artistic-2.0 MD5sum: 63da5e711d8adbd89aaa7e98ebeac09c NeedsCompilation: no Package: LRcell Version: 1.15.0 Depends: R (>= 4.1), ExperimentHub, AnnotationHub Imports: BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: ce4351b489a5c27c0995f3f38eae0afa NeedsCompilation: no Package: lumi Version: 2.59.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 28e1ca205848f036da048212f25e96e4 NeedsCompilation: no Package: lute Version: 1.3.0 Depends: R (>= 4.3.0), stats, methods, utils, SummarizedExperiment, SingleCellExperiment, BiocGenerics Imports: S4Vectors, Biobase, scran, dplyr, ggplot2 Suggests: nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray License: Artistic-2.0 MD5sum: b8687466aff61cc3bbb5ba2857027de6 NeedsCompilation: no Package: LymphoSeq Version: 1.35.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 6588aae39db741b0243ef7851eaf756f NeedsCompilation: no Package: M3C Version: 1.29.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: e29d84f459a19b7d3660b91a851de577 NeedsCompilation: no Package: M3Drop Version: 1.33.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: cc80f385313821a8002a83a847d7350d NeedsCompilation: no Package: m6Aboost Version: 1.13.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: fae8b724965d4ea206ac7ef7e375415e NeedsCompilation: no Package: maCorrPlot Version: 1.77.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: f0bbcb146935882624964755d530fb4a NeedsCompilation: no Package: MACSQuantifyR Version: 1.21.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: 9ef89ae19d9e9ecd54e2fc6bd6fd3133 NeedsCompilation: no Package: MACSr Version: 1.15.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: 2a76a759c9641a3fc76c0f9e2bdc9cae NeedsCompilation: no Package: made4 Version: 1.81.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 299454c9160173d1875c7957cdc1c520 NeedsCompilation: no Package: MADSEQ Version: 1.33.0 Depends: R (>= 3.5.0), rjags (>= 4.6) Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: 1bea13413919a5ca6773026477217be2 NeedsCompilation: no Package: maftools Version: 2.23.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, curl License: MIT + file LICENSE MD5sum: 18a09feeacc5f123dd0bfadf466fbd29 NeedsCompilation: yes Package: magpie Version: 1.7.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE MD5sum: ddbf635aebbf9eb2adc5ca4d196282a7 NeedsCompilation: no Package: magrene Version: 1.9.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: f2d799330e076b034554601ca78a7e16 NeedsCompilation: no Package: MAI Version: 1.13.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: d6c551de5de0d3ef93bdbb99bbe46aae NeedsCompilation: no Package: MAIT Version: 1.41.0 Depends: R (>= 2.10), CAMERA, Rcpp, pls Imports: gplots,e1071,class,MASS,plsgenomics,agricolae,xcms,methods,caret Suggests: faahKO Enhances: rgl License: GPL-2 MD5sum: cf000a22ce3df1611fd5baa5df66347d NeedsCompilation: no Package: makecdfenv Version: 1.83.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: 68ae66482d2a629691bc4c394d722c5b NeedsCompilation: yes Package: MANOR Version: 1.79.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 MD5sum: ae88a458aeb7a3c5f8126ece30b161cf NeedsCompilation: yes Package: MantelCorr Version: 1.77.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 1340722a0b75db9b6e0e7cc933b5a886 NeedsCompilation: no Package: MAPFX Version: 1.3.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 3de62c929db78d0e5eee7a6f9987ff80 NeedsCompilation: no Package: maPredictDSC Version: 1.45.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: 23436536a1c669e8bae065e6d8a14c0e NeedsCompilation: no Package: mapscape Version: 1.31.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7d22d916214ef55aea2d28e48805b932 NeedsCompilation: no Package: mariner Version: 1.7.0 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData License: GPL-3 MD5sum: cf9eb7c62347bee10b72f2c94b965573 NeedsCompilation: no Package: marr Version: 1.17.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: 4a75724c83dd168bddd9d8e5992cd476 NeedsCompilation: yes Package: marray Version: 1.85.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: e49a983ac059de43679075ec7db44546 NeedsCompilation: no Package: martini Version: 1.27.0 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown License: GPL-3 MD5sum: 842f347bba4d11e375539b5c8ffe5212 NeedsCompilation: yes Package: maser Version: 1.25.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE MD5sum: fbf8d77080dbbcb35e1f93eb9a14e7c8 NeedsCompilation: no Package: maSigPro Version: 1.79.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: c46be9077376258985c443dc727794ac NeedsCompilation: no Package: maskBAD Version: 1.51.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: b95b5b7b5925e303cef710b5d2b9444b NeedsCompilation: no Package: MassArray Version: 1.59.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: b98aead862bab7acec1cff74f78a9710 NeedsCompilation: no Package: massiR Version: 1.43.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: ddba7ec47ba72d95cb843fd873946f33 NeedsCompilation: no Package: MassSpecWavelet Version: 1.73.0 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 5639fc948cbc87179db9643ab6cf62ac NeedsCompilation: yes Package: MAST Version: 1.33.0 Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress, Matrix Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr License: GPL (>= 2) MD5sum: 32f6eba6564fd970099df0d9e2beaa44 NeedsCompilation: no Package: mastR Version: 1.7.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR License: MIT + file LICENSE MD5sum: 252eee1ddc99ee4911e84c7a0135e774 NeedsCompilation: no Package: matchBox Version: 1.49.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 7504469c7453fac03c630e09963ca421 NeedsCompilation: no Package: MatrixGenerics Version: 1.19.0 Depends: matrixStats (>= 1.4.1) Imports: methods Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: b2071f9f5549f0bd15d7b2f230eff839 NeedsCompilation: no Package: MatrixQCvis Version: 1.15.0 Depends: DT (>= 0.33), SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0) Imports: ComplexHeatmap (>= 2.7.9), dplyr (>= 1.0.5), ExperimentHub (>= 2.6.0), ggplot2 (>= 3.3.3), grDevices (>= 4.1.0), Hmisc (>= 4.5-0), htmlwidgets (>= 1.5.3), impute (>= 1.65.0), imputeLCMD (>= 2.0), limma (>= 3.47.12), MASS (>= 7.3-58.1), methods (>= 4.1.0), pcaMethods (>= 1.83.0), proDA (>= 1.5.0), rlang (>= 0.4.10), rmarkdown (>= 2.7), Rtsne (>= 0.15), shinydashboard (>= 0.7.1), shinyhelper (>= 0.3.2), shinyjs (>= 2.0.0), stats (>= 4.1.0), sva (>= 3.52.0), tibble (>= 3.1.1), tidyr (>= 1.1.3), umap (>= 0.2.7.0), UpSetR (>= 1.4.0), vsn (>= 3.59.1) Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), httr (>= 1.4.7), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) License: GPL-3 MD5sum: 7258db01c4ff90f9f63112c3dab430ef NeedsCompilation: no Package: MatrixRider Version: 1.39.0 Depends: R (>= 3.1.2) Imports: methods, TFBSTools, IRanges, XVector, Biostrings LinkingTo: IRanges, XVector, Biostrings, S4Vectors Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 License: GPL-3 MD5sum: c4847c22fad2b69f68b7d3fc3bb15b2c NeedsCompilation: yes Package: matter Version: 2.9.0 Depends: R (>= 4.4), BiocParallel, Matrix, methods Imports: BiocGenerics, ProtGenerics, digest, irlba, stats, stats4, graphics, grDevices, parallel, utils LinkingTo: BH Suggests: BiocStyle, knitr, testthat, plotly License: Artistic-2.0 | file LICENSE MD5sum: 1ce1af1cecdec1bbe9e139a90695f40d NeedsCompilation: yes Package: MBAmethyl Version: 1.41.0 Depends: R (>= 2.15) License: Artistic-2.0 MD5sum: ff2716b3d2938644363eefcf8deeb5e0 NeedsCompilation: no Package: MBASED Version: 1.41.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 697dcb91cdc8971e69c0a5486536c7c4 NeedsCompilation: no Package: MBCB Version: 1.61.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: c700a207dac0eba122cf49509ed28184 NeedsCompilation: no Package: mbkmeans Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix, BiocParallel LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 9e40b317b70dfc708c339aba2d0b4b5a NeedsCompilation: yes Package: mBPCR Version: 1.61.0 Depends: oligoClasses, GWASTools Imports: Biobase, graphics, methods, utils, grDevices Suggests: xtable License: GPL (>= 2) MD5sum: d823908377a8c5be1a9b2c25a36707b7 NeedsCompilation: no Package: MBQN Version: 2.19.0 Depends: R (>= 3.6) Imports: stats, graphics, utils, limma (>= 3.30.13), SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0), BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData, rmarkdown Suggests: knitr License: GPL-3 + file LICENSE MD5sum: cc3d7aaf1b2951dc9ce4a89b3f257db4 NeedsCompilation: no Package: MBttest Version: 1.35.0 Depends: R (>= 3.3.0), stats, gplots, gtools,graphics,base, utils,grDevices Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: f2d4086110f55e17d7345e8cb59d2017 NeedsCompilation: no Package: MCbiclust Version: 1.31.0 Depends: R (>= 3.4) Imports: BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 MD5sum: 4659db6642e5713b4d7bf8a7e9f3ac48 NeedsCompilation: no Package: mdp Version: 1.27.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 MD5sum: 588ab4d7442accae88bd5e9d980ec566 NeedsCompilation: no Package: mdqc Version: 1.69.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: fc049aaeeda5d92ceaf9fce4d7bfef1e NeedsCompilation: no Package: MDTS Version: 1.27.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 MD5sum: 28425c9dd25093d6107d0cc9a782e8bd NeedsCompilation: no Package: MEAL Version: 1.37.0 Depends: R (>= 3.6.0), Biobase, MultiDataSet Imports: GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 MD5sum: dedc3428aacb39a205b0526c49b4d42d NeedsCompilation: no Package: MeasurementError.cor Version: 1.79.0 License: LGPL MD5sum: dcaa2d67fc9df1c6bf5e718ab80e69aa NeedsCompilation: no Package: MEAT Version: 1.19.0 Depends: R (>= 4.0) Imports: impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0), grDevices, graphics, stats, utils, stringr, tibble, RPMM (>= 1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 8bb2b1e7c10068df11a3eb7f301580b8 NeedsCompilation: no Package: MEB Version: 1.21.0 Depends: R (>= 3.6.0) Imports: e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment Suggests: knitr,rmarkdown,BiocStyle License: GPL-2 MD5sum: f9dca4ee9030303b13f6c2d9b4408cba NeedsCompilation: no Package: MEDIPS Version: 1.59.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) MD5sum: 6e2e0bf791cb1f5b8f86c554685c8eb1 NeedsCompilation: no Package: MEDME Version: 1.67.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) MD5sum: cbda960041707868b250c4ce738b3fd0 NeedsCompilation: yes Package: megadepth Version: 1.17.0 Imports: xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 MD5sum: aad19f0a9047a62d2421b6d9f6af1124 NeedsCompilation: no Package: MEIGOR Version: 1.41.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 MD5sum: 7815f22ea399df020271024135d76611 NeedsCompilation: no Package: Melissa Version: 1.23.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, mclust, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 87343b3d5cbab1919694bd3d7770bc40 NeedsCompilation: no Package: memes Version: 1.15.0 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: 234b6f00b317a9645289b0a2d7e98930 NeedsCompilation: no Package: Mergeomics Version: 1.35.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8f674d70061e68b3b5b0ca8b790fbc37 NeedsCompilation: no Package: MeSHDbi Version: 1.43.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: e5ed009cacf9955b5b767ea0ed0e79cf NeedsCompilation: no Package: meshes Version: 1.33.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: fd832c17ee3212d61c969dfd173b078a NeedsCompilation: no Package: meshr Version: 2.13.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 MD5sum: 9ff5c4327428edbd764ceb42460fb78d NeedsCompilation: no Package: MesKit Version: 1.17.0 Depends: R (>= 4.0.0) Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 075ff91e7f217840b51e32fde48aef05 NeedsCompilation: no Package: messina Version: 1.43.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: b65784727fd19bb657c1b19caa1b17ac NeedsCompilation: yes Package: metabCombiner Version: 1.17.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 45cb07d515c3f0429c1f56bb845bb569 NeedsCompilation: yes Package: metabinR Version: 1.9.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6c7384560261ef376c9202d803b1cf51 NeedsCompilation: no Package: MetaboAnnotation Version: 1.11.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: f73ca7d3dccdd48d502e3e0206a9fae4 NeedsCompilation: no Package: MetaboCoreUtils Version: 1.15.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 MD5sum: a2426892090d2a6dbe93d0a4460e8dea NeedsCompilation: no Package: metabolomicsWorkbenchR Version: 1.17.0 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: 246e73924cf2c8511a44523b28721ec0 NeedsCompilation: no Package: metabomxtr Version: 1.41.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 28e7955f78ad73da48c11e90b94c36ad NeedsCompilation: no Package: MetaboSignal Version: 1.37.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 6a7bba34e719c3c949dc28f4f2f8f886 NeedsCompilation: no Package: metaCCA Version: 1.35.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 88769fb8eca66677a89e1ad14cd6c966 NeedsCompilation: no Package: MetaCyto Version: 1.29.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: e647a7d4b668f6bec0f8e3b3180cb833 NeedsCompilation: no Package: metagene2 Version: 1.23.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 368fe76b0052ba6800b2c546db3234e4 NeedsCompilation: no Package: metahdep Version: 1.65.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: e77a3bf50c2297d6876c9f58552166d9 NeedsCompilation: yes Package: metaMS Version: 1.43.0 Depends: R (>= 4.0), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics, graphics, stats, utils Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: 0502c32326efc36cd9dbbfcff2291688 NeedsCompilation: no Package: MetaNeighbor Version: 1.27.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: 22151c9d5519939d9718fc25825d775d NeedsCompilation: no Package: MetaPhOR Version: 1.9.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: d4d489f98830118b0968c75f6ccea5f3 NeedsCompilation: no Package: metapod Version: 1.15.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 83055b599c8739cef63a9715b7024ec0 NeedsCompilation: yes Package: metapone Version: 1.13.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: c6d646b0b9e814967c1a78eee4da9cd7 NeedsCompilation: no Package: metaSeq Version: 1.47.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 8d614846aea4a4df54b6abc1ea578648 NeedsCompilation: no Package: metaseqR2 Version: 1.19.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 626d4e5baa42c294306423099ac2e57b NeedsCompilation: yes Package: MetCirc Version: 1.37.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 1fddca9edfc5ebb0a015e28297366668 NeedsCompilation: no Package: methimpute Version: 1.29.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: f46dc5293a86c0863ac128d35e338c4e NeedsCompilation: yes Package: MethPed Version: 1.35.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: ede50947817c844604e578df05c1340b NeedsCompilation: no Package: MethReg Version: 1.17.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader License: GPL-3 MD5sum: 1778e4faf112a29a20b0735a383248ab NeedsCompilation: no Package: methrix Version: 1.21.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 951d21b904aafafc8e8d367f5d3b0e42 NeedsCompilation: no Package: MethTargetedNGS Version: 1.39.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: 5afeaea1d57c8a230f658e49b5a3b97b NeedsCompilation: no Package: MethylAid Version: 1.41.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 89d2ad8277efe9fcbffe1f74a8a6e7c1 NeedsCompilation: no Package: methylCC Version: 1.21.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 0f251a910b62982276cf18939c553e25 NeedsCompilation: no Package: methylclock Version: 1.13.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: d1bfc0736c547fc4faf5fe26d5fb224d NeedsCompilation: yes Package: methylGSA Version: 1.25.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: ee554c9854b75d29eb846989d4ecf7ae NeedsCompilation: no Package: methyLImp2 Version: 1.3.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5c7b3cd77349f038770508aa536085d3 NeedsCompilation: no Package: MethylMix Version: 2.37.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 79cb2a389812aa8a9504b8f336fadcd5 NeedsCompilation: no Package: methylMnM Version: 1.45.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 146c0c3f7a0fde28cf65238fb4176c24 NeedsCompilation: yes Package: methylPipe Version: 1.41.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 9e13412107e56ef86841dd664400369e NeedsCompilation: yes Package: methylscaper Version: 1.15.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: 0ef9c5099e9e130e40d4e4a2bb480fc1 NeedsCompilation: no Package: MethylSeekR Version: 1.47.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 84f4645d7ced612df68dab046006111f NeedsCompilation: no Package: methylSig Version: 1.19.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: c1800d6484851cf0105f11f7a20e675d NeedsCompilation: no Package: methylumi Version: 2.53.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 31cc8c7298e5e9841808cf20d5baa8d2 NeedsCompilation: no Package: MetID Version: 1.25.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: ea17309fd7fc3ebe061d85dcec0c97bf NeedsCompilation: no Package: MetMashR Version: 1.1.0 Depends: R (>= 4.3.0), struct Imports: dplyr, methods, httr, scales, ggthemes, ggplot2, utils, rlang, cowplot, stats Suggests: covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, ChemmineOB, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, RVenn, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx License: GPL-3 MD5sum: 2542c9686fad9562d67df4419c4679a1 NeedsCompilation: no Package: MetNet Version: 1.25.0 Depends: R (>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: 8621732d1186aacdb2650d01ec8263fa NeedsCompilation: no Package: mfa Version: 1.29.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: a67a938b85c271eee088bd744cde3b2e NeedsCompilation: yes Package: Mfuzz Version: 2.67.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 0b43e9ae45320117984fa5c57bcfeb9b NeedsCompilation: no Package: MGFM Version: 1.41.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: f97c6d5399eec487078e8de969698eae NeedsCompilation: no Package: MGFR Version: 1.33.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 856241c3a0436d2983ce4a6f70287cfa NeedsCompilation: no Package: MGnifyR Version: 1.3.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: 0babca2499c753a778cd83618a0533ac NeedsCompilation: no Package: mgsa Version: 1.55.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 5fc28fbf350fc811940cde8bb5c85bde NeedsCompilation: yes Package: mia Version: 1.15.6 Depends: R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: 141908abcab70c2571bfea04ffd4fb4d NeedsCompilation: no Package: miaSim Version: 1.13.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 0c7431bc8644aef121f5aaf96542d4dd NeedsCompilation: no Package: miaViz Version: 1.15.2 Depends: R (>= 4.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports: ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggplot2, ggraph, ggtree, methods, rlang, scater, S4Vectors, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 8ac1b3ed5b1babc2491920f7a642ca27 NeedsCompilation: no Package: MiChip Version: 1.61.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 4cbbe78f97364667ee4dc2ebb4bc549b NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.13.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 3ff817046593001a77935a80cca99b6d NeedsCompilation: no Package: MicrobiotaProcess Version: 1.19.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: 8825c1a383ddd335a51218b5b16eeee2 NeedsCompilation: no Package: microRNA Version: 1.65.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 795ddd271ac80d7fce95e13387370d70 NeedsCompilation: yes Package: microSTASIS Version: 1.7.0 Depends: R (>= 4.2.0) Imports: BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: 799daca72ae582ee03265a331de93605 NeedsCompilation: no Package: MICSQTL Version: 1.5.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: d55d30ed4d380e2402b880c71b358e77 NeedsCompilation: no Package: midasHLA Version: 1.15.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: 61ec868e8abeb24fb6c006ac8f4f12be NeedsCompilation: no Package: miloR Version: 2.3.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: c790f0f45dc67696dbabf619b2205035 NeedsCompilation: yes Package: mimager Version: 1.31.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 7e367bff081b072678f5a2b536d73c2c NeedsCompilation: no Package: mina Version: 1.15.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: 8f10396e8d39186158bb3c75315c649d NeedsCompilation: yes Package: MineICA Version: 1.47.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: bf39ae61deb73fffdda3a3a8b7a335ea NeedsCompilation: no Package: minet Version: 3.65.0 Imports: infotheo License: Artistic-2.0 MD5sum: 99e8824bddd66161401595f5b9e1fdb4 NeedsCompilation: yes Package: minfi Version: 1.53.1 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: c22693e1aff1841fdbcffaa6282166d8 NeedsCompilation: no Package: MinimumDistance Version: 1.51.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 6c446d351a854c25de7b9cd7848bf916 NeedsCompilation: no Package: MiPP Version: 1.79.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 00a2e2ed6c1148ed40aa7ad33ce803f2 NeedsCompilation: no Package: miQC Version: 1.15.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: ca67888bba35670b75acf030ff0af54f NeedsCompilation: no Package: MIRA Version: 1.29.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 0538d6088b26105cb62f537d3a409580 NeedsCompilation: no Package: MiRaGE Version: 1.49.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 34d1d98a87d6700f85bd7d68e29f8667 NeedsCompilation: no Package: miRBaseConverter Version: 1.31.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 8af75bd48820d767827c48df9c187f62 NeedsCompilation: no Package: miRcomp Version: 1.37.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: fc5d44e1b95b91ffcdf4aec16bc7f2e3 NeedsCompilation: no Package: mirIntegrator Version: 1.37.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 743b6444050b42ee24034c9c9549767f NeedsCompilation: no Package: MIRit Version: 1.3.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 79b5da64cf134ce0232c4c6873b094e7 NeedsCompilation: yes Package: miRLAB Version: 1.37.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 480edb6ab8ee3290d8b96efb20418223 NeedsCompilation: no Package: miRNAmeConverter Version: 1.35.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: fdc01469baf2925d054a4d02ecad0b93 NeedsCompilation: no Package: miRNApath Version: 1.67.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 763f8cf122ffc9d261bc827e60f77d34 NeedsCompilation: no Package: miRNAtap Version: 1.41.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 63262de4887759a5cae1ffbf02f2c939 NeedsCompilation: no Package: miRSM Version: 2.3.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: cd76f3ef01f5d2a392b8b476f68e648f NeedsCompilation: yes Package: miRspongeR Version: 2.11.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 0f1b678ed813c4c15ef45e35c02c79e4 NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.15.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 971c94fc259fce478aec52cbb7b75bde NeedsCompilation: no Package: missMethyl Version: 1.41.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: d54daf2292df496b0b30973b8aaa27a8 NeedsCompilation: no Package: missRows Version: 1.27.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 25d78c7e290b7a15bfe385d05d1ce732 NeedsCompilation: no Package: mistyR Version: 1.15.0 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost License: GPL-3 MD5sum: b05d468c6b542805b9a2f5ad6f453bc9 NeedsCompilation: no Package: mitoClone2 Version: 1.13.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 2cb47a06670bc0200fd9dda643c53b3e NeedsCompilation: yes Package: mixOmics Version: 6.31.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, gsignal, rgl Suggests: BiocStyle, knitr, rmarkdown, testthat, microbenchmark, magick License: GPL (>= 2) MD5sum: a180decbfaf23cb4803c8135c33c8afa NeedsCompilation: no Package: MLInterfaces Version: 1.87.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: 0ff110bf271f614007d2da209f554f57 NeedsCompilation: no Package: MLP Version: 1.55.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: a47af6ec8389d393f63eb638b6f065ae NeedsCompilation: no Package: MLSeq Version: 2.25.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 0b555115dc4fccffda24aeab8e231544 NeedsCompilation: no Package: MMDiff2 Version: 1.35.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 95b1132e7c1a771c13ac15a2e6bc1c79 NeedsCompilation: no Package: mnem Version: 1.23.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: e2246018c10efeaef8ce1c30a031c07b NeedsCompilation: yes Package: moanin Version: 1.15.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 9dd4b481d1521d2db2c558b427bf9a31 NeedsCompilation: no Package: mobileRNA Version: 1.3.0 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 907d073bcfa05a20e658fbc20b5c5124 NeedsCompilation: no Package: MODA Version: 1.33.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 0dd0d8530b1692218fd70975f3c0f459 NeedsCompilation: no Package: ModCon Version: 1.15.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: efddabe88c0a481318b2e408fb9111d9 NeedsCompilation: no Package: Modstrings Version: 1.23.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 3d33a97a2cffb1100e508c979acca450 NeedsCompilation: no Package: MOFA2 Version: 1.17.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: 1e79cc54a97aaa0f33e40ee21a84802b NeedsCompilation: yes Package: MOGAMUN Version: 1.17.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 5aef2862885955f563882c8b85c4578b NeedsCompilation: no Package: mogsa Version: 1.41.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 5511debeb0e35d73f3eb9b0aba832576 NeedsCompilation: no Package: MoleculeExperiment Version: 1.7.0 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7172a79d20705d6a44b8a527b7f48b4c NeedsCompilation: no Package: MOMA Version: 1.19.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 6ecda9e59b439a8d406630c820c53ef8 NeedsCompilation: no Package: monaLisa Version: 1.13.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot, RSQLite Suggests: JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL (>= 3) MD5sum: 66b2b0ce14185fcf4455c0a4dad74c7c NeedsCompilation: no Package: monocle Version: 2.35.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: c086fffdc67fac83696c419f2c65b470 NeedsCompilation: yes Package: Moonlight2R Version: 1.5.0 Depends: R (>= 4.3), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: 9dd69bb2b82b46579f9561f982c66dca NeedsCompilation: no Package: MoonlightR Version: 1.33.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: f241d49777f3c3056102beff18f3edc7 NeedsCompilation: no Package: mosaics Version: 2.45.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: dd506943324f7d75456f812653505e15 NeedsCompilation: yes Package: mosbi Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 58b3ebff2c6f295d02bc4345a37c893a NeedsCompilation: yes Package: MOSClip Version: 1.1.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 1fbf147a8d3216b22125600ec23fe926 NeedsCompilation: no Package: mosdef Version: 1.3.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: fca822f6cb41f0d3cc265f228b3a8ed3 NeedsCompilation: no Package: MOSim Version: 2.3.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: 2f58b2bf23b7a3bfe11716c6b3944ad6 NeedsCompilation: yes Package: Motif2Site Version: 1.11.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: 2b9d46dad244176b365c4d8d79f31594 NeedsCompilation: no Package: motifbreakR Version: 2.21.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: 9fdf33eaa1dd098155fa573a39abcc82 NeedsCompilation: no Package: motifcounter Version: 1.31.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 0d381bd7135b436646920100113f46f0 NeedsCompilation: yes Package: MotifDb Version: 1.49.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: e480594498cb1bcae2cd9e57f4427eef NeedsCompilation: no Package: motifmatchr Version: 1.29.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: df20eee2c1360463a4fa803ba4a16a69 NeedsCompilation: yes Package: motifStack Version: 1.51.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: 669ed040f9178c17ba06411cf70c622e NeedsCompilation: no Package: motifTestR Version: 1.3.1 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 159d32b8823e3f122d9aeed982053e6d NeedsCompilation: no Package: MouseFM Version: 1.17.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 6837b92bc761521efaa75c2d2a75372f NeedsCompilation: no Package: MPAC Version: 1.1.0 Depends: R (>= 4.4.0) Imports: data.table (>= 1.14.2), SummarizedExperiment (>= 1.30.2), BiocParallel (>= 1.28.3), fitdistrplus (>= 1.1), igraph (>= 1.4.3), BiocSingular (>= 1.10.0), S4Vectors (>= 0.32.3), SingleCellExperiment (>= 1.16.0), bluster (>= 1.4.0), fgsea (>= 1.20.0), scran (>= 1.22.1), ComplexHeatmap (>= 2.16.0), grid, stats Suggests: rmarkdown, knitr, svglite, bookdown(>= 0.34), testthat (>= 3.0.0) License: GPL-3 MD5sum: 223ff26999fa1ba659ad11d2831fce42 NeedsCompilation: no Package: MPFE Version: 1.43.0 License: GPL (>= 3) MD5sum: fa116110e11e331c446f82b8aba12381 NeedsCompilation: no Package: mpra Version: 1.29.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 51cfa1dd391f8882b8f32fdd0b60b054 NeedsCompilation: no Package: MPRAnalyze Version: 1.25.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 8b4a43db43ae08b83a24c4c6c460701f NeedsCompilation: no Package: msa Version: 1.39.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: bb2e03698c501ce0adde620dd0b94574 NeedsCompilation: yes Package: MSA2dist Version: 1.11.1 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: f42df85858d4c2d3a5fda4b48bdf21c2 NeedsCompilation: yes Package: MsBackendMassbank Version: 1.15.0 Depends: R (>= 4.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 5ec3e25d2dee236b13109a5136555b7a NeedsCompilation: no Package: MsBackendMetaboLights Version: 1.1.0 Depends: R (>= 4.2.0), Spectra (>= 1.15.12) Imports: curl, ProtGenerics, BiocFileCache, S4Vectors, methods Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: bd1c9dc61bc5048c2c7cd9c7048a04ea NeedsCompilation: no Package: MsBackendMgf Version: 1.15.1 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: c3c4e49ab53acb840a11f172e0770fe7 NeedsCompilation: no Package: MsBackendMsp Version: 1.11.0 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 2742a5e244c10f432d24abc5851857e1 NeedsCompilation: no Package: MsBackendRawFileReader Version: 1.13.1 Depends: R (>= 4.1), methods, Spectra (>= 1.15.10) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.13.1), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 1b5c402dbf65a6265481b2a05757092b NeedsCompilation: yes Package: MsBackendSql Version: 1.7.1 Depends: R (>= 4.2.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, stringi, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: c0baf4f741f07856c4988f82040df6ef NeedsCompilation: no Package: MsCoreUtils Version: 1.19.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: 5ca22cfd359ea7d765e28f45d184058f NeedsCompilation: yes Package: MsDataHub Version: 1.7.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: 71c3c78d324145a83a831e90b58a0369 NeedsCompilation: no Package: MsExperiment Version: 1.9.0 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 MD5sum: 4cab680c929a4d0020f8dd703e6eeada NeedsCompilation: no Package: MsFeatures Version: 1.15.0 Depends: R (>= 4.1) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3607e6d9b7f1694f876e59f09fafa109 NeedsCompilation: no Package: msgbsR Version: 1.31.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: a7967b5a29d89101b3721b884007a2bf NeedsCompilation: no Package: msImpute Version: 1.17.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: b4763d49a01f3f0bc622212b8497ca70 NeedsCompilation: no Package: mslp Version: 1.9.0 Depends: R (>= 4.2.0) Imports: data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest License: GPL-3 MD5sum: 9a8e2d83d966760d465e1fb900f68b2f NeedsCompilation: no Package: msmsEDA Version: 1.45.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 669f1d42b72544607956faf5d98266c7 NeedsCompilation: no Package: msmsTests Version: 1.45.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue Suggests: xtable License: GPL-2 MD5sum: 4d417dc06f3f9985677f8843f5d5cd5a NeedsCompilation: no Package: MSnbase Version: 2.33.2 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1) Imports: MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment, Spectra License: Artistic-2.0 MD5sum: ecf2045311a83a3cf0795c35eb20e6b8 NeedsCompilation: yes Package: MSnID Version: 1.41.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable License: Artistic-2.0 MD5sum: ce3e90b4b981d7e679ae742a19e6de81 NeedsCompilation: no Package: mspms Version: 0.99.5 Depends: R (>= 4.4.0) Imports: QFeatures, SummarizedExperiment, magrittr, rlang, dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo, heatmaply, readr, rstatix, tibble, ggpubr, imputeLCMD Suggests: knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 80cb04fdd356f0d56a0cea251b55f8ce NeedsCompilation: no Package: MSPrep Version: 1.17.0 Depends: R (>= 4.1.0) Imports: SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), crmn, preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, missForest, sva, VIM, Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 MD5sum: aee1b9f3b7822c6a1815a634342214eb NeedsCompilation: no Package: msPurity Version: 1.33.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: b8cb1ac24bcd199e0a5c453a6bc71c02 NeedsCompilation: no Package: msqrob2 Version: 1.15.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: aa7e1468ef6b249d177b29f02ac9f18c NeedsCompilation: no Package: MsQuality Version: 1.7.0 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) License: GPL-3 MD5sum: 753bef765dd70f9c2cf1a5a24a5ff810 NeedsCompilation: no Package: MSstats Version: 4.15.0 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, plotly, marray, stats, grDevices, graphics, methods, statmod, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown, mockery License: Artistic-2.0 MD5sum: 8ea12f7e763a4e29041c175b11ec7521 NeedsCompilation: yes Package: MSstatsBig Version: 1.5.0 Imports: arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: c3002316043715283b27f4a4771a9965 NeedsCompilation: no Package: MSstatsConvert Version: 1.17.0 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: 568218da4fb30651e3f48da2ebd9afd0 NeedsCompilation: no Package: MSstatsLOBD Version: 1.15.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: 823aa6c839ecfe76c20b60573dcb2445 NeedsCompilation: no Package: MSstatsQC Version: 2.25.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: 370bcc5f149d778873363af83bf0a59d NeedsCompilation: no Package: MSstatsQCgui Version: 1.27.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 4c0fa732e4260fd8af17101766107483 NeedsCompilation: no Package: MSstatsTMT Version: 2.15.1 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 54787a7b82dcc55e7e0759a5de43f0d8 NeedsCompilation: no Package: MuData Version: 1.11.0 Depends: Matrix, S4Vectors, rhdf5 Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 MD5sum: 7999b99c97e87f5a129bcf9ddb59fd6e NeedsCompilation: no Package: Mulcom Version: 1.57.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: b7e70e7d6a6df45746ee345d52fa8068 NeedsCompilation: yes Package: MultiAssayExperiment Version: 1.33.1 Depends: SummarizedExperiment (>= 1.3.81), R (>= 3.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: eb7003297ad5e2241c2be9b557f210a0 NeedsCompilation: no Package: MultiBaC Version: 1.17.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: fb8ba80f2156a4c502c9cb17ee10a2fb NeedsCompilation: no Package: multiClust Version: 1.37.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 868b295c1be5befb4057896ec60c0237 NeedsCompilation: no Package: multicrispr Version: 1.17.0 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 32cd929a2819e0605eb05c63c9cd7cc3 NeedsCompilation: no Package: MultiDataSet Version: 1.35.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: d2a318cce05873cad8a7a9be91c6ed25 NeedsCompilation: no Package: multiGSEA Version: 1.17.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: db9c88e012feabba11776464bfdbdb2b NeedsCompilation: no Package: multiHiCcompare Version: 1.25.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 1fe82ca51339595182302435441c1ee0 NeedsCompilation: no Package: MultiMed Version: 2.29.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 48a0a7fcb67017cf1144eb755ad4170b NeedsCompilation: no Package: multiMiR Version: 1.29.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: 2d3d9b1ee6c26900075aef22a6f00903 NeedsCompilation: no Package: MultimodalExperiment Version: 1.7.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: d09ed84d87473852430d6bb8cabf009c NeedsCompilation: no Package: MultiRNAflow Version: 1.5.0 Depends: Mfuzz (>= 2.58.0), R (>= 4.3) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.14.0), DESeq2 (>= 1.38.1), factoextra (>= 1.0.7), FactoMineR (>= 2.6), ggalluvial (>= 0.12.3), ggplot2 (>= 3.4.0), ggplotify (>= 0.1.2), ggrepel (>= 0.9.2), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4), plot3Drgl (>= 1.0.3), reshape2 (>= 1.4.4), S4Vectors (>= 0.36.2), stats (>= 4.2.2), SummarizedExperiment (>= 1.28.0), UpSetR (>= 1.4.0), utils (>= 4.2.2) Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 | file LICENSE MD5sum: 458417663840e6c3de32e10cfc393072 NeedsCompilation: no Package: multiscan Version: 1.67.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 28304602c7eb1a50f32aff98300e9eb6 NeedsCompilation: yes Package: multistateQTL Version: 1.3.0 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, data.table, collapse Imports: methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: ee030fbf2762baba14e5fc1f9ef72285 NeedsCompilation: no Package: multiWGCNA Version: 1.5.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 69e3eb1596d6f70b6c2861302a9f994c NeedsCompilation: no Package: multtest Version: 2.63.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: be7aca1943b19bca8473ab3a9ae64e32 NeedsCompilation: yes Package: mumosa Version: 1.15.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: 6f503d8cd183b1dabe19e1daa63dd0d7 NeedsCompilation: no Package: MungeSumstats Version: 1.15.2 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: 092a9b07cd9c3588d401e191b82f7645 NeedsCompilation: no Package: muscat Version: 1.21.0 Depends: R (>= 4.4) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR License: GPL-3 MD5sum: b12eed2af5c7172844ea91e2b61b9d61 NeedsCompilation: no Package: muscle Version: 3.49.0 Depends: Biostrings License: Unlimited MD5sum: 144d601eea9a36461e1c4c31db78a254 NeedsCompilation: yes Package: musicatk Version: 2.1.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales, conclust Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 9ddb9df34fa7487261a5925cca11b3ac NeedsCompilation: no Package: MutationalPatterns Version: 3.17.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: cb6e81e6ada005066c267820a8a284aa NeedsCompilation: no Package: MVCClass Version: 1.81.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 21893935ad32913fe46c1fb2ad4164e3 NeedsCompilation: no Package: MWASTools Version: 1.31.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 5ed75f82cb770ab70c0c620c4b30033f NeedsCompilation: no Package: mygene Version: 1.43.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: 6949c47dba9ad742603226325aa74f70 NeedsCompilation: no Package: myvariant Version: 1.37.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 87210f6ba43340b0f6946a05edba0514 NeedsCompilation: no Package: mzID Version: 1.45.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 4fed8b4cc7058bb0fd5a0863c1b28ecb NeedsCompilation: no Package: mzR Version: 2.41.1 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: b964425b3bbd683ae916b60865565985 NeedsCompilation: yes Package: NADfinder Version: 1.31.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: dfcfd756d9a1b057ea71d8c7c05d3ad1 NeedsCompilation: no Package: NanoMethViz Version: 3.3.0 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: e23392fc80d7c7d293146c0821421322 NeedsCompilation: yes Package: NanoStringDiff Version: 1.37.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: fd9c7ddb654eab15b7b39e125d3c5edd NeedsCompilation: yes Package: NanoStringNCTools Version: 1.15.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: 83604c71b14e0e5766bad817719a44a1 NeedsCompilation: no Package: NanoTube Version: 1.13.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE MD5sum: 4cc02ed05ecf1af624142d6d468586c1 NeedsCompilation: no Package: NBAMSeq Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: abab2b087a76451bb6e6571ed2bc0dcc NeedsCompilation: no Package: ncdfFlow Version: 2.53.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 1d7f8df7d33533de25ff85eea5495b2b NeedsCompilation: yes Package: ncGTW Version: 1.21.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: ab868ba3f17505a26b0b5116f87cc27d NeedsCompilation: yes Package: NCIgraph Version: 1.55.0 Depends: R (>= 4.0.0) Imports: graph, KEGGgraph, methods, RBGL, RCy3, R.oo Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 6b0e8d949277d08403424779584cc26e NeedsCompilation: no Package: ncRNAtools Version: 1.17.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: 5faa7ae333b4fcb0f345bd8243b29433 NeedsCompilation: no Package: ndexr Version: 1.29.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 87271ed2fb58adcf2a91fa67b0cdc54a NeedsCompilation: no Package: nearBynding Version: 1.17.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 8196a3fee43b7189be10dc2571f6437f NeedsCompilation: no Package: Nebulosa Version: 1.17.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: d4aa735b6712adec7c40f4b11bee5344 NeedsCompilation: no Package: nempi Version: 1.15.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: 3a9a4a76d1c66dbeb6318fb976bf4e6a NeedsCompilation: no Package: NetActivity Version: 1.9.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: 54ea588982b8187960f92539230b9213 NeedsCompilation: no Package: netboost Version: 2.15.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, BiocStyle, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: 1e40f74b6ce418c58afe29fc3aefd3c4 NeedsCompilation: yes Package: nethet Version: 1.39.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: c63e0e882caea11af11d8eebba01e156 NeedsCompilation: yes Package: NetPathMiner Version: 1.43.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 30a0eabaf2f269d8dc4f3487313b9bfd NeedsCompilation: yes Package: netprioR Version: 1.33.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 7bd5c4c40d2144d6f3fcc8d2b707529f NeedsCompilation: no Package: netresponse Version: 1.67.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 558241aae920cf98f6d80e09b6363628 NeedsCompilation: yes Package: NetSAM Version: 1.47.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: 3bb23fdb9594b014d78082ff32f3efc0 NeedsCompilation: no Package: netSmooth Version: 1.27.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: 194984c4e926d64b87e37446df6b9299 NeedsCompilation: no Package: NewWave Version: 1.17.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: d622f6a38e2c1a03c3aff17f6fd0556d NeedsCompilation: no Package: ngsReports Version: 2.9.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: 55b5f3b0553180ef1f656f6e201115c4 NeedsCompilation: no Package: nipalsMCIA Version: 1.5.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 06a83809f35e407ad1501510b20e2c2c NeedsCompilation: no Package: nnNorm Version: 2.71.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 4c1fd87352174e61b49cc88ed980223b NeedsCompilation: no Package: nnSVG Version: 1.11.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 218b6c64f04970dd34a2a965981a3f2b NeedsCompilation: no Package: NOISeq Version: 2.51.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 4b1fbace1be3e90f1f2893dc73a1bf6c NeedsCompilation: no Package: NoRCE Version: 1.19.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE MD5sum: b2066a1609888adcb5bd47e6f7240b2a NeedsCompilation: no Package: normalize450K Version: 1.35.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 78484d03102ea8c39d04117448bd2b97 NeedsCompilation: no Package: NormalyzerDE Version: 1.25.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 98e96afa5fc4b9ea485284bcdc2f5aed NeedsCompilation: no Package: NormqPCR Version: 1.53.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 0432eadf6037ee41bc21dfebfaaf7d60 NeedsCompilation: no Package: normr Version: 1.33.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: 393c7ceb3efa5ec4f9e7e0fca3546aea NeedsCompilation: yes Package: NPARC Version: 1.19.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 13cf50fe79a1a2db0b4b40e37f9ab2c7 NeedsCompilation: no Package: npGSEA Version: 1.43.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: fc99ca3500439255b5e38f2e20b3ab47 NeedsCompilation: no Package: NTW Version: 1.57.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 7738655c0d448bc2a87e4a1fb50e4dbf NeedsCompilation: no Package: nucleoSim Version: 1.35.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 1e78d58be37b69699a2144aa06c1c63e NeedsCompilation: no Package: nucleR Version: 2.39.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: bc7c033a79a42ac8e58571d47700e343 NeedsCompilation: no Package: nuCpos Version: 1.25.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: 6d0e72d7066c2d6c91d88e7874b55efe NeedsCompilation: yes Package: nullranges Version: 1.13.0 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment License: GPL-3 MD5sum: 5980e2646decf5d6c0bdd149e810420c NeedsCompilation: no Package: NuPoP Version: 2.15.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7f5f067ac4d6c00f11b2268b57b3b9ed NeedsCompilation: yes Package: occugene Version: 1.67.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: 6eebfe10442f3c757a3ebb0dac4874fd NeedsCompilation: no Package: OCplus Version: 1.81.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL MD5sum: 23dee7a7069666cd5179cbd06af28655 NeedsCompilation: no Package: octad Version: 1.9.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: ef7599273b99997b87f05720915b9b4b NeedsCompilation: no Package: odseq Version: 1.35.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: 5b6cb03994667432b1986fd1df905296 NeedsCompilation: no Package: OGRE Version: 1.11.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 MD5sum: 3b3ecdf353e81735378038f40666bce6 NeedsCompilation: no Package: oligo Version: 1.71.0 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 5d1e895194461fc917a0dbe2cc58ea77 NeedsCompilation: yes Package: oligoClasses Version: 1.69.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 73401f7f1c51d7554ee9a98bbce1ee71 NeedsCompilation: no Package: OLIN Version: 1.85.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: ddfcf6f50ba1cd6309668ae7279f83d4 NeedsCompilation: no Package: OLINgui Version: 1.81.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: 46217904e7b2610c3c5d0432573f3f71 NeedsCompilation: no Package: omada Version: 1.9.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>= 0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2), clValid(>= 0.7) Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: d15e85b820a271eeff7a9a584a9ca784 NeedsCompilation: no Package: OmaDB Version: 2.23.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: f6e1f4ca353ab611a8b41583836a37b4 NeedsCompilation: no Package: omicade4 Version: 1.47.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 MD5sum: 4d54298833335f07f5a47553bac29bb7 NeedsCompilation: no Package: OmicCircos Version: 1.45.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: d21546f0aa2e3c8f3321fbc83fcbad61 NeedsCompilation: no Package: omicplotR Version: 1.27.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 2acf081db8a439edb112a30b510060d3 NeedsCompilation: no Package: omicRexposome Version: 1.29.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: a82506f29faf3c15f6561fd146e6397a NeedsCompilation: no Package: OmicsMLRepoR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: dplyr, stringr, rols, tidyr, methods, stats, tibble, data.tree, jsonlite, plyr, BiocFileCache, readr, DiagrammeR, rlang, lubridate Suggests: arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>= 3.0.0), cBioPortalData License: Artistic-2.0 MD5sum: 19eee3829e249de8d683a368c3ccb747 NeedsCompilation: no Package: OMICsPCA Version: 1.25.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: cd2fee889fd952ef082f84dda7cdb928 NeedsCompilation: no Package: omicsPrint Version: 1.27.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: df82c7bf6bcb8e9a92a503c8b96ddc99 NeedsCompilation: no Package: omicsViewer Version: 1.11.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: b12d1e5ddfb7b060e23706530bbc13cf NeedsCompilation: no Package: Omixer Version: 1.17.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: cbc36a3ac0bee6ebcb1fc14fb995316d NeedsCompilation: no Package: OmnipathR Version: 3.15.0 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: 4424da5802837e2b0ba6bf1d3ab7f4a6 NeedsCompilation: no Package: ompBAM Version: 1.11.0 Imports: utils, Rcpp Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 08954273a47228a1a4f3b9f52faaff79 NeedsCompilation: no Package: omXplore Version: 1.1.0 Depends: R (>= 4.4.0), methods Imports: shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, DT, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: cbe09f47688846c8becd1c92636c84b4 NeedsCompilation: no Package: oncomix Version: 1.29.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 8c70422ced1f22bf8be74b31c95377ac NeedsCompilation: no Package: oncoscanR Version: 1.9.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 73a4e5e5706d0624c02639c4d5ac0c60 NeedsCompilation: no Package: OncoScore Version: 1.35.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 952893ee51d57b2ec77a4aed5d3ee264 NeedsCompilation: no Package: OncoSimulR Version: 4.9.0 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 7b88637a9b22f94bceec029c3acf3ecd NeedsCompilation: yes Package: onlineFDR Version: 2.15.0 Imports: stats, Rcpp, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: dd4b56870118f4d8731d2efb251d6191 NeedsCompilation: yes Package: ontoProc Version: 2.1.0 Depends: R (>= 4.0), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick License: Artistic-2.0 MD5sum: 2341e794a8a31408edf8ff8ee1fcdedc NeedsCompilation: no Package: openCyto Version: 2.19.0 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowClust(>= 3.11.4),RBGL,graph,data.table,RColorBrewer LinkingTo: cpp11, BH Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: d4b4654b2def87fe087a41e10c13385e NeedsCompilation: yes Package: openPrimeR Version: 1.29.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: 14375d1dd4c8ddafdf2775398c0e254b NeedsCompilation: no Package: OpenStats Version: 1.19.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 9197e2e31d99ebf3a27d563acb3348ed NeedsCompilation: no Package: oposSOM Version: 2.25.0 Depends: R (>= 4.0.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: 93a1d4b0056b2feb6f34a41c140e6272 NeedsCompilation: yes Package: oppar Version: 1.35.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: 356013bd608cd54e83058297509c6ecd NeedsCompilation: yes Package: oppti Version: 1.21.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT MD5sum: b8803010bb70e46442aef7bfb14e3d1a NeedsCompilation: no Package: optimalFlow Version: 1.19.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 14e9c96630d7057a9c5586169d620834 NeedsCompilation: no Package: OPWeight Version: 1.29.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: b69c46c788876529773682b2bdd88f52 NeedsCompilation: no Package: OrderedList Version: 1.79.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: c5b12b717a1773d869b1d4c8075cb2da NeedsCompilation: no Package: ORFhunteR Version: 1.15.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 8834a241709a6322d9aa5ea77b9f68d3 NeedsCompilation: yes Package: ORFik Version: 1.27.0 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 709c3e3aec6f453744d2acff3d61b2aa NeedsCompilation: yes Package: Organism.dplyr Version: 1.35.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: a91589455b17be13cd08d528b5d6ba72 NeedsCompilation: no Package: OrganismDbi Version: 1.49.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4aa38d81398e5a18a5ed24cf8fa2c833 NeedsCompilation: no Package: orthogene Version: 1.13.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: a71963eb973cb0358dee15502cd1be41 NeedsCompilation: no Package: orthos Version: 1.5.0 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 99ae7fcc71a95598350c2b220de55f25 NeedsCompilation: no Package: OSAT Version: 1.55.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 636c6226ebcfb56bd45541e7b6b6d81c NeedsCompilation: no Package: Oscope Version: 1.37.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 0c7dacec4fbdf82d5870e4747f5667f0 NeedsCompilation: no Package: OTUbase Version: 1.57.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: ba08a023ed03b520f05579ce106622c4 NeedsCompilation: no Package: OUTRIDER Version: 1.25.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, txdbmaker, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: MIT + file LICENSE MD5sum: d2bd205b414f05b962cb4e8d4e155d67 NeedsCompilation: yes Package: OutSplice Version: 1.7.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: bc725943a2aba04b2c96c30856e8679d NeedsCompilation: no Package: OVESEG Version: 1.23.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 915166a7f654b4fa6e079f7ad7b14bb5 NeedsCompilation: yes Package: PAA Version: 1.41.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 6098d128913b6756d61e858d2d20929b NeedsCompilation: yes Package: packFinder Version: 1.19.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 8f06714849bb5ba3498d410c69e69051 NeedsCompilation: no Package: padma Version: 1.17.0 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 License: GPL (>= 3) MD5sum: 6b830ddfa63666563e192c7bc2662305 NeedsCompilation: no Package: PADOG Version: 1.49.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: b42d3d3feb242d6d55fb186527714ffc NeedsCompilation: no Package: pageRank Version: 1.17.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: 913d55480cc276763cdf3a8e3bc2d4a4 NeedsCompilation: no Package: PAIRADISE Version: 1.23.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 3ba6733408cd21c4e9093a12d9603a32 NeedsCompilation: no Package: paircompviz Version: 1.45.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: 1bccb1b4b17524e686c637831a989cc9 NeedsCompilation: no Package: pairkat Version: 1.13.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, KEGGREST, igraph, data.table, methods, stats, magrittr, CompQuadForm, tibble Suggests: rmarkdown, knitr, BiocStyle, dplyr License: GPL-3 MD5sum: 4325f6c96e87f495048fe6fac6007811 NeedsCompilation: no Package: pandaR Version: 1.39.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr, rmarkdown License: GPL-2 MD5sum: af18caf13f999ab456520a5797e71d58 NeedsCompilation: no Package: panelcn.mops Version: 1.29.0 Depends: R (>= 3.5.0), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) MD5sum: cb2152e9229ddb655680d651ceb77fce NeedsCompilation: no Package: PanomiR Version: 1.11.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, GSEABase, igraph, limma, metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer, rlang, tibble, withr, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8ebf4e0fd1ee13a553461e4c9f610fe6 NeedsCompilation: no Package: panp Version: 1.77.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: 49d0949c7c1ee6ddfbb2decf970d8b25 NeedsCompilation: no Package: PANR Version: 1.53.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: a8a5312ac394f0746f8ef4763b84b50e NeedsCompilation: no Package: parglms Version: 1.39.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 84500c1c24dd38aeceb7fd51e0a7c08d NeedsCompilation: no Package: parody Version: 1.65.0 Depends: R (>= 3.5.0), tools, utils Suggests: knitr, BiocStyle, testthat, rmarkdown License: Artistic-2.0 MD5sum: 8ede48e4892dc3fafc4b54e6cd446c53 NeedsCompilation: no Package: partCNV Version: 1.5.0 Depends: R (>= 3.5.0) Imports: stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges, BiocStyle Suggests: rmarkdown, knitr, IRanges, testthat (>= 3.0.0) License: GPL-2 MD5sum: ebfc294b4460c1f4fe327838b919405c NeedsCompilation: no Package: PAST Version: 1.23.0 Depends: R (>= 4.0) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors Suggests: knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 5f1adab9a9693847affa9c5035448570 NeedsCompilation: no Package: Path2PPI Version: 1.37.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: 08ee33182780a4e9b2017e40a2c50c58 NeedsCompilation: no Package: pathifier Version: 1.45.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 MD5sum: 46f4edddd7b93233e71e9af2ba12979f NeedsCompilation: no Package: pathlinkR Version: 1.3.1 Depends: R (>= 4.4.0) Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea, ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr, sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork Suggests: AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr License: GPL-3 + file LICENSE MD5sum: f138d72f0c2f69eecc7b7fb53d380700 NeedsCompilation: no Package: PathNet Version: 1.47.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: 3f844bd364cd35018e489dfb7ac5271f NeedsCompilation: no Package: pathRender Version: 1.75.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 0cbc76fe9cdd7c646cd32db07efd931a NeedsCompilation: no Package: pathview Version: 1.47.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 9e8d5717bad51eff47f15437bf5f7b31 NeedsCompilation: no Package: pathwayPCA Version: 1.23.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: c9b8548305539cf09cfec2bea8f5ad22 NeedsCompilation: no Package: pcaExplorer Version: 3.1.0 Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: e0522e54dc1676f9c1067f5461875606 NeedsCompilation: no Package: pcaMethods Version: 1.99.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 9a8028d07e3e47b07536447e63b27a1f NeedsCompilation: yes Package: PCAN Version: 1.35.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: 0e41d4de64ae2d667c93486dff99f455 NeedsCompilation: no Package: PCAtools Version: 2.19.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: cc3aca422a7670cfcacc8f245832182a NeedsCompilation: yes Package: pdInfoBuilder Version: 1.71.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: 7bd23b8817673b3401969e8610d7e320 NeedsCompilation: yes Package: PeacoQC Version: 1.17.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) MD5sum: 3fb67dc5649ee0bf34237458d98f6c0f NeedsCompilation: no Package: peakPantheR Version: 1.21.0 Depends: R (>= 4.2) Imports: foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.5.0), gridExtra (>= 2.3), MSnbase (>= 2.4.0), mzR (>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>= 3.98.1.10), minpack.lm (>= 1.2.1), scales(>= 0.5.0), shiny (>= 1.0.5), bslib, shinycssloaders (>= 1.0.0), DT (>= 0.15), pracma (>= 2.2.3), utils, lubridate, svglite (>= 2.1.1) Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle License: GPL-3 MD5sum: 7df6dc0f574354126eb32278ab88a15f NeedsCompilation: no Package: PECA Version: 1.43.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) MD5sum: 698fe50dbcb3d8de2d42260d3fc62062 NeedsCompilation: no Package: peco Version: 1.19.0 Depends: R (>= 3.5.0) Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: a8432650393b347d3fe0ef977082af7b NeedsCompilation: no Package: Pedixplorer Version: 1.3.0 Depends: R (>= 4.3.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl, shinyWidgets, htmlwidgets, DT, gridExtra, data.table, plotly, colourpicker, shinytoastr, scales, shinycssloaders Suggests: diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, covr, devtools, R.devices, usethis, magick License: Artistic-2.0 MD5sum: 1d72f0b86401255f086e3804b98a32a3 NeedsCompilation: no Package: pengls Version: 1.13.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 9c0e1a94eae933b8a586de201837ee4c NeedsCompilation: no Package: PepSetTest Version: 1.1.0 Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr License: GPL (>= 3) MD5sum: 04384970b0f71ad64b08f8019d7c0043 NeedsCompilation: no Package: PepsNMR Version: 1.25.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: 1a9a4e00ce260319bcb0305d11d70d94 NeedsCompilation: no Package: pepStat Version: 1.41.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: d9d212c1dee6c80bd62c1a700fa15ab0 NeedsCompilation: no Package: pepXMLTab Version: 1.41.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 7f25228aa3ff2f5610b1678d1f62b31c NeedsCompilation: no Package: periodicDNA Version: 1.17.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: dd5471fd6c8ba8bb2648ade9a4d836c3 NeedsCompilation: no Package: pfamAnalyzeR Version: 1.7.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 61e05c3f8192fb73363aec580d3d00f3 NeedsCompilation: no Package: pgca Version: 1.31.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: ea1413ca8dd1506e6274a9720c1fb075 NeedsCompilation: no Package: pgxRpi Version: 1.3.0 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: 16e6c4632b6789d73740f03eec6ab32d NeedsCompilation: no Package: phantasus Version: 1.27.0 Depends: R (>= 4.3) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm, tidyr, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 251ef56c68e9b599d3f5a3471ba8714a NeedsCompilation: no Package: phantasusLite Version: 1.5.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: fd8d806e071afd34e789ec317d6eacf2 NeedsCompilation: no Package: PharmacoGx Version: 3.11.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: 77c099ec07fef81cbf07d6067ec38843 NeedsCompilation: yes Package: PhenoGeneRanker Version: 1.15.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: d67d1cb5eca340dadfaa929569d52ac2 NeedsCompilation: no Package: phenomis Version: 1.9.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 3e030601a777810746bece09d6b18892 NeedsCompilation: no Package: phenopath Version: 1.31.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: ae11f42533ed419a97c605c801e6509d NeedsCompilation: yes Package: phenoTest Version: 1.55.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: ad7433b2a2569ca5236d13dfdd842412 NeedsCompilation: no Package: PhenStat Version: 2.43.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: c670458808ee1712479274c77d7fcc45 NeedsCompilation: no Package: philr Version: 1.33.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: ae358b71a0587942eb951bfa5aef03a1 NeedsCompilation: no Package: PhIPData Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 736836e503fa9bf41b12d19dcf0fe4a3 NeedsCompilation: no Package: phosphonormalizer Version: 1.31.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: e953f26c9a6c2b642be2d7dea0c7c8e9 NeedsCompilation: no Package: PhosR Version: 1.17.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: 8c51a271394cc0f3a2baa7c6bafd887f NeedsCompilation: no Package: PhyloProfile Version: 1.21.3 Depends: R (>= 4.4.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 97a616cb9e15ac400f898ffc0bd4b4e8 NeedsCompilation: no Package: piano Version: 2.23.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 727d3e0215591903753a9c0a496a1b42 NeedsCompilation: no Package: pickgene Version: 1.79.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 6bbda0aa1e802ed3c0edea51085e4675 NeedsCompilation: no Package: PICS Version: 2.51.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: b49c50d8c987aad52b362f8d3f1aaf63 NeedsCompilation: yes Package: Pigengene Version: 1.33.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 050912e566a8158668fdefa7d4e0c260 NeedsCompilation: no Package: PING Version: 2.51.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: f1657891f0d0c8e351e0c7d98c2cf868 NeedsCompilation: yes Package: pipeComp Version: 1.17.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 4d2a416922c1e854599a3a8e7f3d1941 NeedsCompilation: no Package: pipeFrame Version: 1.23.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 78dfa5108d8ab4bec68e3689ea0e46b8 NeedsCompilation: no Package: PIPETS Version: 1.3.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: b62e90e81f9d8dfe85e90174e1923a57 NeedsCompilation: no Package: Pirat Version: 1.1.0 Depends: R (>= 4.4.0) Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: e553be7913a5dec9229358fbecae7d97 NeedsCompilation: no Package: PIUMA Version: 1.3.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: 66ddb6542f3cedc09413f19990d74783 NeedsCompilation: no Package: planet Version: 1.15.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: de5f658379c638846c5722771a890267 NeedsCompilation: no Package: planttfhunter Version: 1.7.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 95f64f35cbe8f43c06bb0412c0f0324f NeedsCompilation: no Package: plasmut Version: 1.5.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 39e0441b62e666be7c8ff0d024314f35 NeedsCompilation: no Package: plgem Version: 1.79.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: abbbf59b5ea8ba40f0ac9db31d87054c NeedsCompilation: no Package: plier Version: 1.77.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 9193f6732b7c7b8addfe830fcababd32 NeedsCompilation: yes Package: plotgardener Version: 1.13.0 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 69bb01123c35ec6a4f6947bf3eb01465 NeedsCompilation: yes Package: plotGrouper Version: 1.25.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: adf99f4b400e11c66ba6cc495b60bd90 NeedsCompilation: no Package: PLPE Version: 1.67.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: c4145d9517d53e227f50c2c4be01a6bf NeedsCompilation: no Package: PLSDAbatch Version: 1.3.0 Depends: R (>= 4.3.0) Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment Suggests: knitr, rmarkdown, testthat, badger License: GPL-3 MD5sum: 5904dd74ec8c6f1632c6bbcca6d3a371 NeedsCompilation: no Package: plyinteractions Version: 1.5.0 Depends: R (>= 4.3.0) Imports: InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges, plyranges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR License: Artistic-2.0 MD5sum: fd2780d22463a7397c06e7ebf4790daa NeedsCompilation: no Package: plyranges Version: 1.27.0 Depends: R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4) Imports: methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>= 0.23.10), utils Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 License: Artistic-2.0 MD5sum: 1b2883ffbc37ad7e9a239cbef8039da0 NeedsCompilation: no Package: plyxp Version: 1.1.0 Depends: R (>= 4.4.0) Imports: dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect, vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods Suggests: devtools, knitr, rmarkdown, testthat, airway, IRanges, here License: MIT + file LICENSE MD5sum: 7d1e304690c2214ba3cb9415e7bb6671 NeedsCompilation: no Package: pmm Version: 1.39.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: e2270507c716d3e4785926617dc26ff0 NeedsCompilation: no Package: pmp Version: 1.19.0 Depends: R (>= 4.0) Imports: stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick License: GPL-3 MD5sum: 145f0039af37615c079899701089144f NeedsCompilation: no Package: PoDCall Version: 1.15.0 Depends: R (>= 4.4) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: b75d2399878b8de5a3f467f5828d848e NeedsCompilation: no Package: podkat Version: 1.39.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: 01c5b204f945fe381aa8a79e6fafd662 NeedsCompilation: yes Package: pogos Version: 1.27.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ae9ade175e1e50290abb8da64e125d80 NeedsCompilation: no Package: POMA Version: 1.17.5 Depends: R (>= 4.0) Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, fgsea, FSA, ggcorrplot, ggplot2, ggrepel, glmnet, impute, janitor, limma, lme4, magrittr, MASS, mixOmics, multcomp, msigdbr, purrr, randomForest, RankProd (>= 3.14), rlang, SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) License: GPL-3 MD5sum: b737ad60f2e6ff74d364497a00fc8fac NeedsCompilation: no Package: powerTCR Version: 1.27.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 46d05d3c988bf7c7a5cdb8cbf17a3bc3 NeedsCompilation: no Package: POWSC Version: 1.15.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: a8cd43bbcb478fa51243052d481aab73 NeedsCompilation: no Package: ppcseq Version: 1.15.0 Depends: R (>= 4.1.0), rstan (>= 2.18.1) Imports: benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics, lifecycle, magrittr, methods, parallel, purrr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1), stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 MD5sum: 382847209aa36d954475bc8f93ca0d28 NeedsCompilation: yes Package: PPInfer Version: 1.33.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 MD5sum: aa4af44aa93dd2991cb66c45cb74faeb NeedsCompilation: no Package: pqsfinder Version: 2.23.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 0cbb6128c492db712c55c9630d778d0f NeedsCompilation: yes Package: pram Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 765ad2106222d172507d6ed779f7c844 NeedsCompilation: no Package: preciseTAD Version: 1.17.0 Depends: R (>= 4.1) Imports: S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle License: MIT + file LICENSE MD5sum: ce54edc02fd0738c76318d3cf8feb551 NeedsCompilation: no Package: PREDA Version: 1.53.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 MD5sum: 51faf9b4e46d160c22b03c2c0a6f9411 NeedsCompilation: no Package: preprocessCore Version: 1.69.0 Imports: stats License: LGPL (>= 2) MD5sum: 67dffc12c57539b7af1c55ed1f402b4c NeedsCompilation: yes Package: primirTSS Version: 1.25.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: abb8f9ca0b4f7415339dc9863e3154c8 NeedsCompilation: no Package: PrInCE Version: 1.23.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 1f79ec02bb0f7bc1a40dbc292c22c7c5 NeedsCompilation: no Package: proActiv Version: 1.17.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang, scales, S4Vectors, SummarizedExperiment, stats, tibble, txdbmaker Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra License: MIT + file LICENSE MD5sum: 77db3f2e44f6cce3f3c995ca7e9f9230 NeedsCompilation: no Package: proBAMr Version: 1.41.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi Imports: GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e60f0517e79ed7e8f95b3b997d570a7d NeedsCompilation: no Package: PROcess Version: 1.83.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 MD5sum: 6aacc35c850924a9938ec4369469ebfc NeedsCompilation: no Package: procoil Version: 2.35.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) MD5sum: 42e2e19a611452dfcb35ad61fd4e8aef NeedsCompilation: no Package: proDA Version: 1.21.0 Imports: stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 3bca55e262bdd78c44e90af360115493 NeedsCompilation: no Package: profileplyr Version: 1.23.0 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices, rlang, tiff, Rsamtools Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo License: GPL (>= 3) MD5sum: c72c8b046fb887b7d65a1403617f6eeb NeedsCompilation: no Package: profileScoreDist Version: 1.35.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE MD5sum: 57672ed4ebe5320940497f1f278bf60e NeedsCompilation: yes Package: progeny Version: 1.29.0 Depends: R (>= 3.6.0) Imports: Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: ef34f73577f32f56e639edbd94662f35 NeedsCompilation: no Package: projectR Version: 1.23.0 Depends: R (>= 4.0.0) Imports: methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: 465358714c25c92f66a1b00378a77cff NeedsCompilation: no Package: pRoloc Version: 1.47.0 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 MD5sum: af7c0654f25bb16e49828e9bcf897153 NeedsCompilation: yes Package: pRolocGUI Version: 2.17.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 639d599de1a6e98701f23bec3f33de2b NeedsCompilation: no Package: PROMISE Version: 1.59.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: fe0812324d1bf3e89cf1caec04dde0eb NeedsCompilation: no Package: PRONE Version: 1.1.0 Depends: R (>= 4.4.0), SummarizedExperiment Imports: dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors, ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS, edgeR, matrixStats, preprocessCore, stats, gtools, methods, ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2, plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2, POMA, ggtext, scales, DEqMS Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT License: GPL (>= 3) MD5sum: 486c01e08876c3a98b7bebecdac126aa NeedsCompilation: no Package: PROPER Version: 1.39.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL MD5sum: c964bd3a2f3d364a914b15dfa6ee69ed NeedsCompilation: no Package: Prostar Version: 1.39.0 Depends: R (>= 4.4.0) Imports: DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase, DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown, rclipboard, sass, shinyTree, shinyWidgets Suggests: BiocStyle, BiocManager, testthat, knitr License: Artistic-2.0 MD5sum: acac777655eb0c2e2c802244e693ebfc NeedsCompilation: no Package: proteinProfiles Version: 1.47.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: 43c93507ef65d5ee526becd1b101b5cb NeedsCompilation: no Package: ProteoDisco Version: 1.13.0 Depends: R (>= 4.1.0), Imports: BiocGenerics (>= 0.38.0), BiocParallel (>= 1.26.0), Biostrings (>= 2.60.1), checkmate (>= 2.0.0), cleaver (>= 1.30.0), dplyr (>= 1.0.6), GenomeInfoDb (>= 1.28.0), GenomicFeatures (>= 1.44.0), GenomicRanges (>= 1.44.0), IRanges (>= 2.26.0), methods (>= 4.1.0), ParallelLogger (>= 2.0.1), plyr (>= 1.8.6), rlang (>= 0.4.11), S4Vectors (>= 0.30.0), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation (>= 1.36.0), XVector (>= 0.32.0), Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) License: GPL-3 MD5sum: 3ff14a333982a899931da030ef695100 NeedsCompilation: no Package: ProteoMM Version: 1.25.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: b96b2bb4857aa4c65545fdd66ac728ff NeedsCompilation: no Package: protGear Version: 1.11.0 Depends: R (>= 4.2), dplyr (>= 0.8.0) , limma (>= 3.40.2) ,vsn (>= 3.54.0) Imports: magrittr (>= 1.5) , stats (>= 3.6) , ggplot2 (>= 3.3.0) , tidyr (>= 1.1.3) , data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2) , tibble (>= 3.1.0) , rmarkdown (>= 2.9) , knitr (>= 1.33), utils (>= 3.6), genefilter (>= 1.74.0), readr (>= 2.0.1) , Biobase (>= 2.52.0), plyr (>= 1.8.6) , Kendall (>= 2.2) , shiny (>= 1.0.0) , purrr (>= 0.3.4), plotly (>= 4.9.0) , MASS (>= 7.3) , htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , grid(>= 4.1.1), styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , rlang (>= 0.4.11), remotes (>= 2.4.0) Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) License: GPL-3 MD5sum: 269870311b841582528ebec7f656cfe5 NeedsCompilation: no Package: ProtGenerics Version: 1.39.0 Depends: methods Suggests: testthat License: Artistic-2.0 MD5sum: 1be9f5fd513aedba63b2ed895339f5c7 NeedsCompilation: no Package: PSMatch Version: 1.11.0 Depends: S4Vectors Imports: utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat License: Artistic-2.0 MD5sum: b54aaf81037c7ee6841d382974f940e8 NeedsCompilation: no Package: ptairMS Version: 1.15.0 Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls License: GPL-3 MD5sum: 8ff7a8ef9e447ce26604f01d75893990 NeedsCompilation: yes Package: puma Version: 3.49.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 7ef752f3191f2af949664db9fea58d85 NeedsCompilation: yes Package: PureCN Version: 2.13.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 MD5sum: 76e88eff149fbe6ec2c25703cf36706f NeedsCompilation: no Package: pvac Version: 1.55.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: 28db7ae5b3626e451570ba4bcfad4ccd NeedsCompilation: no Package: pvca Version: 1.47.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 52e80e3a883f32cb79df8b0669f3e1b1 NeedsCompilation: no Package: Pviz Version: 1.41.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 999aebafd833140d35394093abcf2479 NeedsCompilation: no Package: pwalign Version: 1.3.0 Depends: BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5) Imports: methods, utils LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: 1a50f55d805133527af90e8f4100ed97 NeedsCompilation: yes Package: PWMEnrich Version: 4.43.0 Depends: R (>= 3.5.0), methods, BiocGenerics, Biostrings Imports: grid, seqLogo, gdata, evd, S4Vectors Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: ff9f616f6794f12dcc06a05b9a648720 NeedsCompilation: no Package: qckitfastq Version: 1.23.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: 6bd30344a96d2bf6504adc4b186693e5 NeedsCompilation: yes Package: qcmetrics Version: 1.45.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown, markdown License: GPL-2 MD5sum: 7d66c42e45be3062eb8ce9d22a3472d8 NeedsCompilation: no Package: QDNAseq Version: 1.43.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 License: GPL MD5sum: 7abc85b32baec305b2df159070546dc3 NeedsCompilation: no Package: QFeatures Version: 1.17.0 Depends: R (>= 4.0), MultiAssayExperiment Imports: methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2 Suggests: SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 MD5sum: 8f208ea61f23edb332b5de639719b1a7 NeedsCompilation: no Package: qmtools Version: 1.11.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: eda7ca7629203de48d56e0b34254e62b NeedsCompilation: no Package: qpcrNorm Version: 1.65.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: 966b13adfe8bf2a60ca8e5492a8a8051 NeedsCompilation: no Package: qpgraph Version: 2.41.0 Depends: R (>= 3.5) Imports: methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 0908cdb5d46feea69b05dc5244bb5116 NeedsCompilation: yes Package: qPLEXanalyzer Version: 1.25.0 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: patchwork, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: 8727493ce796834804210d5d7c4391c2 NeedsCompilation: no Package: qsea Version: 1.33.0 Depends: R (>= 4.3) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS License: GPL-2 MD5sum: b46f4621eb7c84d4bc88bf08afca86a0 NeedsCompilation: yes Package: qsmooth Version: 1.23.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics, Hmisc Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: dcb908e2b2ed0f360c8d900932e4f14a NeedsCompilation: no Package: QSutils Version: 1.25.0 Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL-2 MD5sum: 12e80d52960292478c3a3ae9210bbaad NeedsCompilation: no Package: qsvaR Version: 1.11.0 Depends: R (>= 4.2), SummarizedExperiment Imports: sva, stats, ggplot2, rlang, tidyverse, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 521e1c728af017b23bcea8de93624ddb NeedsCompilation: no Package: QTLExperiment Version: 1.5.0 Depends: SummarizedExperiment Imports: methods, rlang, checkmate, dplyr, collapse, vroom, tidyr, tibble, utils, stats, ashr, S4Vectors, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: efe18092707b6e0d128bb9e058d870a7 NeedsCompilation: no Package: Qtlizer Version: 1.21.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 1aee7fa5be6e6fb0615e2f046113a0d5 NeedsCompilation: no Package: quantiseqr Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble License: GPL-3 MD5sum: ef4bdb9123538637df083941686b3237 NeedsCompilation: no Package: quantro Version: 1.41.0 Depends: R (>= 4.0) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 46bad2499177025d4db46886efc27fcc NeedsCompilation: no Package: quantsmooth Version: 1.73.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: 1b2cf6d3435441c532c9722da025636d NeedsCompilation: no Package: QuasR Version: 1.47.0 Depends: R (>= 4.4), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: c71e00060984e09163fa71b1053fb598 NeedsCompilation: yes Package: QuaternaryProd Version: 1.41.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: 7da483446f7b4af3a2bb465eed3d3d3b NeedsCompilation: yes Package: QUBIC Version: 1.35.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 1c08b2f83cca81766f8808e122286c78 NeedsCompilation: yes Package: qusage Version: 2.41.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans, fftw License: GPL (>= 2) MD5sum: fbad1cdb63b58a208be98e40403623a1 NeedsCompilation: no Package: qvalue Version: 2.39.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL MD5sum: 24c24aa852b2231ebbd3d84102874b48 NeedsCompilation: no Package: R3CPET Version: 1.39.0 Depends: R (>= 3.2), Rcpp (>= 0.10.4), methods Imports: methods, parallel, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), ggbio LinkingTo: Rcpp Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) MD5sum: a45bcf5c51bec0897e1d3b42b72a14d7 NeedsCompilation: yes Package: r3Cseq Version: 1.53.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 MD5sum: c54addc8bbf7b49ff181e4e1d7972ed8 NeedsCompilation: no Package: R453Plus1Toolbox Version: 1.57.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), pwalign, Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: b599d16d4229f56efd20c02d53e4bd9b NeedsCompilation: yes Package: R4RNA Version: 1.35.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 MD5sum: dbd7c06435c71ffe1b4045086bd7602e NeedsCompilation: no Package: RadioGx Version: 2.11.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, data.table, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader Suggests: rmarkdown, BiocStyle, knitr, pander, markdown License: GPL-3 MD5sum: cc6b89140e21713716090da1cceb9733 NeedsCompilation: no Package: raer Version: 1.5.0 Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli LinkingTo: Rhtslib Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE MD5sum: 88f7ab6221a8420c8cc8ff17ba8e64fb NeedsCompilation: yes Package: RaggedExperiment Version: 1.31.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.37.17) Imports: BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment License: Artistic-2.0 MD5sum: 0715d053b392397b180521e13adada5f NeedsCompilation: no Package: RAIDS Version: 1.5.0 Depends: R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS Imports: S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics, ggplot2, stringr Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: Apache License (>= 2) MD5sum: ff975c34e652687ddf26bd951d89fc39 NeedsCompilation: no Package: rain Version: 1.41.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: 6e1065268e4f94955884e1265313a2c9 NeedsCompilation: no Package: ramr Version: 1.15.0 Depends: R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods Imports: IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: ec144b3c9f74f09ee04d8489676fe676 NeedsCompilation: no Package: ramwas Version: 1.31.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 120929b566737999afdd30a5be91c7f3 NeedsCompilation: yes Package: randPack Version: 1.53.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: 0a62eb37c9989f2247a1422dc65f5f41 NeedsCompilation: no Package: randRotation Version: 1.19.0 Imports: methods, graphics, utils, stats, Rdpack (>= 0.7) Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva License: GPL-3 MD5sum: 5505ca6c5cc963c25feb28af16beef76 NeedsCompilation: no Package: RankProd Version: 3.33.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: 2fbf3797ccfaabeab24de692df3cb738 NeedsCompilation: no Package: RAREsim Version: 1.11.0 Depends: R (>= 4.1.0) Imports: nloptr Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0657e2ed67e885c409c847612c489bbf NeedsCompilation: no Package: RareVariantVis Version: 2.35.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: 11798cf2aafceeda262c33ba99d75019 NeedsCompilation: no Package: Rarr Version: 1.7.0 Depends: DelayedArray, BiocGenerics Imports: jsonlite, httr, stringr, R.utils, utils, paws.storage, methods Suggests: BiocStyle, covr, knitr, tinytest, mockery License: MIT + file LICENSE MD5sum: 5861dc24a18bba627358be7e0c1a7716 NeedsCompilation: yes Package: rawDiag Version: 1.3.4 Depends: R (>= 4.4) Imports: dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2, scales, shiny (>= 1.5), stats, utils Suggests: BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat License: GPL-3 MD5sum: cc1aa22c8bfa48736c59dc3895c13d5f NeedsCompilation: no Package: rawrr Version: 1.15.8 Depends: R (>= 4.1) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 7e0d06f3993e7e37fc78c9043e73229f NeedsCompilation: no Package: RbcBook1 Version: 1.75.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: 2adbfcd1ce2f4ff11d33e1f4da3abb74 NeedsCompilation: no Package: Rbec Version: 1.15.0 Imports: Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: df67d205e2c48f8210bca58fd130ec5a NeedsCompilation: yes Package: RBGL Version: 1.83.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 46de6022c5b9eef95b45ba25d6f21829 NeedsCompilation: yes Package: RBioFormats Version: 1.7.0 Imports: EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats Suggests: BiocStyle, knitr, testthat, xml2 License: GPL-3 MD5sum: 113a5a60c00fad0b34f6cfa8121efcbb NeedsCompilation: no Package: RBioinf Version: 1.67.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 MD5sum: e0b0034deb31ffa1de10ba69d186b69b NeedsCompilation: yes Package: rBiopaxParser Version: 2.47.0 Depends: R (>= 4.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph License: GPL (>= 2) MD5sum: a7495cf4ae42e2f93020de3a4515bb4d NeedsCompilation: no Package: rBLAST Version: 1.3.0 Depends: Biostrings (>= 2.26.2) Imports: methods, utils, BiocFileCache Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: bae9c0d983601fa17e419129e40f92fb NeedsCompilation: no Package: RBM Version: 1.39.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) MD5sum: a9ebfb6ae5114a1fb1820269a0b7f74e NeedsCompilation: no Package: Rbowtie Version: 1.47.0 Imports: utils Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 MD5sum: fc8f3f0bd77c816b375eafff7c4c2e5a NeedsCompilation: yes Package: Rbowtie2 Version: 2.13.0 Depends: R (>= 4.1.0) Imports: magrittr, Rsamtools Suggests: knitr, testthat (>= 3.0.0), rmarkdown License: GPL (>= 3) Archs: x64 MD5sum: 8b7028da65c5072bd0d80e370897ab46 NeedsCompilation: yes Package: rbsurv Version: 2.65.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) MD5sum: ead112938961c8ddaba83960e03bbb45 NeedsCompilation: no Package: Rbwa Version: 1.11.0 Depends: R (>= 4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: 099a86b1b6d2cce0acd52917ce040491 NeedsCompilation: yes Package: RCAS Version: 1.33.0 Depends: R (>= 3.5.0), plotly (>= 4.5.2), DT (>= 0.2), data.table Imports: GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, GenomicFeatures, txdbmaker, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot, seqLogo, utils, ranger, gprofiler2 Suggests: testthat, covr, BiocManager License: Artistic-2.0 MD5sum: 3dc884fe331821233a3e869551a129d2 NeedsCompilation: no Package: RCASPAR Version: 1.53.0 License: GPL (>= 3) MD5sum: 83f4f3b7c15dc367660bfeac477766c0 NeedsCompilation: no Package: rcellminer Version: 2.29.0 Depends: R (>= 3.2), Biobase, rcellminerData (>= 2.0.0) Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown License: LGPL-3 + file LICENSE MD5sum: 1dcbf748fd2d10f0f7ad61e95bf7ce51 NeedsCompilation: no Package: rCGH Version: 1.37.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 0250c6588dfb60e936f14cebc9f1cde0 NeedsCompilation: no Package: RcisTarget Version: 1.27.0 Depends: R (>= 3.5.0) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils, zoo Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork Enhances: doMC, doRNG License: GPL-3 MD5sum: b7e87937febf6d2eee990c0cb45107fc NeedsCompilation: no Package: Rcollectl Version: 1.7.0 Imports: utils, ggplot2, lubridate, processx Suggests: knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, testthat, covr License: Artistic-2.0 MD5sum: b962309dcef5a22e0410f25976e32e47 NeedsCompilation: no Package: Rcpi Version: 1.43.0 Depends: R (>= 3.0.2) Imports: Biostrings, GOSemSim, curl, doParallel, foreach, httr2, jsonlite, methods, rlang, stats, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 | file LICENSE MD5sum: 6df0ceb2cdeaeb53bdc9546643f72e1e NeedsCompilation: no Package: RCSL Version: 1.15.0 Depends: R (>= 4.1) Imports: RcppAnnoy, igraph, NbClust, Rtsne, ggplot2(>= 3.4.0), methods, pracma, umap, grDevices, graphics, stats, Rcpp (>= 0.11.0), MatrixGenerics, SingleCellExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse, tinytex License: Artistic-2.0 MD5sum: 0ca7919fd18328629a78938d14b4e130 NeedsCompilation: no Package: Rcwl Version: 1.23.0 Depends: R (>= 3.6), yaml, methods, S4Vectors Imports: utils, stats, BiocParallel, batchtools, DiagrammeR, shiny, R.utils, codetools, basilisk Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 25730dd8dfdde7abf262a4794eaff510 NeedsCompilation: no Package: RcwlPipelines Version: 1.23.0 Depends: R (>= 3.6), Rcwl, BiocFileCache Imports: rappdirs, methods, utils, git2r, httr, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 48be1b696c6184248f04ef5c98f69a06 NeedsCompilation: no Package: RCX Version: 1.11.0 Depends: R (>= 4.2.0) Imports: jsonlite, plyr, igraph, methods Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph License: MIT + file LICENSE MD5sum: f9d2bfb0f80e6f3bdaa48057050f517d NeedsCompilation: no Package: RCy3 Version: 2.27.0 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices License: MIT + file LICENSE MD5sum: 822ab398d91dccc78a65d7469e96615d NeedsCompilation: no Package: RCyjs Version: 2.29.0 Depends: R (>= 3.5.0), BrowserViz (>= 2.7.18), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 06a52938e4d4cc13cff9b6e6f6b4a9be NeedsCompilation: no Package: Rdisop Version: 1.67.3 Depends: R (>= 2.10), Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, RUnit, testthat (>= 3.0.0) License: GPL-2 MD5sum: ddd52f2699c20fb680d8d1a506e391aa NeedsCompilation: yes Package: RDRToolbox Version: 1.57.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) MD5sum: 6ddd29bbf96ec594036bd1a2c9533173 NeedsCompilation: no Package: ReactomeGSA Version: 1.21.0 Imports: jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr, Biobase Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, devtools Enhances: limma, edgeR, Seurat (>= 3.0), scater License: MIT + file LICENSE MD5sum: b48618eaa72ff6e3b94683fb1d75834e NeedsCompilation: no Package: ReactomePA Version: 1.51.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson, yulab.utils (>= 0.1.5) Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat License: GPL-2 MD5sum: b359c61464f7447086da80538ac97176 NeedsCompilation: no Package: ReadqPCR Version: 1.53.0 Depends: R(>= 2.14.0), Biobase, methods Suggests: qpcR License: LGPL-3 MD5sum: 58d2860c7bd23dd4c50048880883d8d8 NeedsCompilation: no Package: REBET Version: 1.25.0 Depends: ASSET Imports: stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 7ec2955f62ee9557e8296d465e1b8b29 NeedsCompilation: yes Package: rebook Version: 1.17.0 Imports: utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends, dir.expiry, filelock, BiocStyle Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows License: GPL-3 MD5sum: 5f6a821169049a126ac6324e39538525 NeedsCompilation: no Package: receptLoss Version: 1.19.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here License: GPL-3 + file LICENSE MD5sum: 409a2b68c935d0d01d4c568cdd94ca2f NeedsCompilation: no Package: recount3 Version: 1.17.0 Depends: SummarizedExperiment Imports: BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount License: Artistic-2.0 MD5sum: 3fc6e64f3ef68704fa4ffe6c75b8bd3c NeedsCompilation: no Package: recountmethylation Version: 1.17.0 Depends: R (>= 4.1) Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub License: Artistic-2.0 MD5sum: 6fd3852c45bccf94508f91f4c9f0afbb NeedsCompilation: no Package: recoup Version: 1.35.0 Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) MD5sum: 274d288281f9edee8e6291be30b0ad12 NeedsCompilation: no Package: RedeR Version: 3.3.0 Depends: R (>= 4.0), methods Imports: scales, igraph Suggests: knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf License: GPL-3 MD5sum: 0d90681342f9c3de58d4510a87d3dc70 NeedsCompilation: no Package: RedisParam Version: 1.9.0 Depends: R (>= 4.2.0), BiocParallel (>= 1.29.12) Imports: methods, redux, withr, futile.logger Suggests: rmarkdown, knitr, testthat, BiocStyle License: Artistic-2.0 MD5sum: 332aa4a4d5d14cdf382c5259ef64b7cb NeedsCompilation: no Package: REDseq Version: 1.53.0 Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils License: GPL (>= 2) MD5sum: 4b27fda1c51a48ff696ce1200214f7e2 NeedsCompilation: no Package: RegEnrich Version: 1.17.0 Depends: R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment Imports: randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat License: GPL (>= 2) MD5sum: 41c3e81843e4f7c4376169a321cb0c4d NeedsCompilation: no Package: regionalpcs Version: 1.5.0 Depends: R (>= 4.3.0) Imports: dplyr, PCAtools, tibble, GenomicRanges Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges License: MIT + file LICENSE MD5sum: e13e89ca540cfac1138f2a0d5ef242c5 NeedsCompilation: no Package: regioneR Version: 1.39.0 Depends: GenomicRanges Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 MD5sum: 4c72576e313fa0f0cab3b66ef50eb944 NeedsCompilation: no Package: regioneReloaded Version: 1.9.0 Depends: R (>= 4.2), regioneR Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6b107eb96910a600c43ac9eccd4041b7 NeedsCompilation: no Package: regsplice Version: 1.33.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 19dd2a9fa1dd90d143a674959fb38330 NeedsCompilation: no Package: regutools Version: 1.19.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: fb0bf5d8129d2616f1bbd74621479d21 NeedsCompilation: no Package: REMP Version: 1.31.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 40ff58a58ae60188430d2d0c872a3678 NeedsCompilation: no Package: Repitools Version: 1.53.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: b3fc35357dcfd7dd162b464c633cf30d NeedsCompilation: yes Package: ReportingTools Version: 2.47.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 4fb3117eff39bbe73f9418abaa821750 NeedsCompilation: no Package: RepViz Version: 1.23.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: dbc91943c40ad97646c089907d5f3a02 NeedsCompilation: no Package: ResidualMatrix Version: 1.17.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: d73abb6733c3ebf028db4fff12602d43 NeedsCompilation: no Package: RESOLVE Version: 1.9.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors, RhpcBLASctl Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 5110c395174a10a28ae3e4f60db963cb NeedsCompilation: no Package: retrofit Version: 1.7.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: a03cc8d8db67766db92067677dfb7004 NeedsCompilation: yes Package: ReUseData Version: 1.7.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: a85e9118e03ac054c845e1cf32b79e39 NeedsCompilation: no Package: rexposome Version: 1.29.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: c5ee8d0c050892cf858b155380a9e660 NeedsCompilation: no Package: rfaRm Version: 1.19.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: fcb01c2a9926079a4f36b54296e84f60 NeedsCompilation: no Package: Rfastp Version: 1.17.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 3c15db628600bbcd771efb38f9a27416 NeedsCompilation: yes Package: rfPred Version: 1.45.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: c5ffc6986cbd93d12b6230ad08715a4e NeedsCompilation: yes Package: rGADEM Version: 2.55.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 MD5sum: 559bc8c7899d2ab42685c6463135ac05 NeedsCompilation: yes Package: rGenomeTracks Version: 1.13.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7332b173122aba65bd5433f741e5ab7e NeedsCompilation: no Package: RgnTX Version: 1.9.0 Depends: R (>= 4.2.0) Imports: GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: b09af6813a26d87f3c4880a3bf308ee3 NeedsCompilation: no Package: rgoslin Version: 1.11.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 54f2c94b77e8bc4316ae8d5687a5f247 NeedsCompilation: yes Package: RGraph2js Version: 1.35.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: 795fb6d4dcc768fafa8d8c2b167403d2 NeedsCompilation: no Package: Rgraphviz Version: 2.51.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 776e346e7b60c800357204f08667b7d4 NeedsCompilation: yes Package: rGREAT Version: 2.9.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: 12a82968fb19422ed94efeeb95ce7619 NeedsCompilation: yes Package: RGSEA Version: 1.41.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 897801f8d580ee6c83e7bda7007e39f1 NeedsCompilation: no Package: rgsepd Version: 1.39.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: 118bef87bd40e58ee0c40dfd5aa5f974 NeedsCompilation: no Package: rhdf5 Version: 2.51.0 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 MD5sum: 1e442a5c416a07e1f7cfb07f0390ff10 NeedsCompilation: yes Package: rhdf5client Version: 1.29.0 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: 88bc7040834dce0d95d3b0552d408e1a NeedsCompilation: yes Package: rhdf5filters Version: 1.19.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE MD5sum: 385e987cd992f8fb40364b35b71d04e1 NeedsCompilation: yes Package: Rhdf5lib Version: 1.29.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: 990d5c9002dde1eb29fd22ca3426127f NeedsCompilation: yes Package: rhinotypeR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: Biostrings Suggests: knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a0e3782802b3b62aa5c8d78de2f7133f NeedsCompilation: no Package: Rhisat2 Version: 1.23.0 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: b9bf564b09b72d8b6e7fc850790693f2 NeedsCompilation: yes Package: Rhtslib Version: 3.3.0 Imports: tools, zlibbioc LinkingTo: zlibbioc Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: 4f30ab6ac7e3dd6409e29f6e94eecb87 NeedsCompilation: yes Package: RiboCrypt Version: 1.13.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, RCurl, shiny, shinycssloaders, shinyhelper, shinyjqui, stringr Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 0acaf3184ace6789b54d50969d6bc811 NeedsCompilation: no Package: RiboDiPA Version: 1.15.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 4a6401a77f7527116a16504a85ec849a NeedsCompilation: yes Package: RiboProfiling Version: 1.37.0 Depends: R (>= 3.5.0), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 2400ff8ebc8097aeb28e2b1c4438c231 NeedsCompilation: no Package: ribor Version: 1.19.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 5c9de7c95e2b68ac4858a2d37dc12b42 NeedsCompilation: no Package: riboSeqR Version: 1.41.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 17e9dc88d0eff23073dc20bf77b89957 NeedsCompilation: no Package: ribosomeProfilingQC Version: 1.19.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: 9513abddef54beb2236eb7d8aa6e2629 NeedsCompilation: no Package: rifi Version: 1.11.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: eac8aac73731b331e011e45a080c0a33 NeedsCompilation: no Package: rifiComparative Version: 1.7.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 08644eebb0005e8118f6539e571fa90e NeedsCompilation: no Package: RImmPort Version: 1.35.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 029d1a61780f961d46c7d4f2cf3112b6 NeedsCompilation: no Package: RITAN Version: 1.31.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: aa61109d4ea33ca850cf01276973ce46 NeedsCompilation: no Package: RIVER Version: 1.31.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: e455c047833de584732e5c246f2763b2 NeedsCompilation: no Package: RJMCMCNucleosomes Version: 1.31.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: ab53922049ec8e02e25204f9f518a852 NeedsCompilation: yes Package: RLassoCox Version: 1.15.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 MD5sum: 3d6e3bbc9bd11855e67f99224cf2736f NeedsCompilation: no Package: RLMM Version: 1.69.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: 4697d703ea82a89c35496b149a7ccfa3 NeedsCompilation: no Package: Rmagpie Version: 1.63.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 755e0cc6baa62303eb2f9d03a0026ecd NeedsCompilation: no Package: RMassBank Version: 3.17.0 Depends: Rcpp Imports: assertthat, Biobase, ChemmineR, data.table, digest, dplyr, enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR, purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble, tidyselect, webchem, XML, yaml Suggests: BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1) License: Artistic-2.0 MD5sum: 1196508cd910156327ea198e8060680c NeedsCompilation: no Package: rmelting Version: 1.23.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: 54b5cca8150dea68ab242948cb25c8e8 NeedsCompilation: no Package: Rmmquant Version: 1.25.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, apeglm, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: e305b16a5953d79a876f5b5862583606 NeedsCompilation: yes Package: RNAdecay Version: 1.27.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: e535ef177169ff43cabf060201d21261 NeedsCompilation: yes Package: rnaEditr Version: 1.17.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: ca3e9611b6bdad96750076d5e6d19ba9 NeedsCompilation: no Package: RNAmodR Version: 1.21.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomicRanges, Modstrings Imports: methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings (>= 2.57.2), BiocParallel, txdbmaker, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 MD5sum: e09dee3b914edbe5c7d6a1f6a017a2b3 NeedsCompilation: no Package: RNAmodR.AlkAnilineSeq Version: 1.21.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 MD5sum: cd8ef38e9f6a7595b7680f8171b885d9 NeedsCompilation: no Package: RNAmodR.ML Version: 1.21.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: 5ebadd980bd152ed8cf31f668f6c6d45 NeedsCompilation: no Package: RNAmodR.RiboMethSeq Version: 1.21.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 MD5sum: ae5b931ff08580629739d5a72824f888 NeedsCompilation: no Package: RNAsense Version: 1.21.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c328859a40ff2f7be5ea695524eda791 NeedsCompilation: no Package: rnaseqcomp Version: 1.37.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f4e5509d8f416be7fe43d4d167c8f60e NeedsCompilation: no Package: RNAseqCovarImpute Version: 1.5.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice Suggests: BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 88d8a6ca5855aad7053fd1394019e3e9 NeedsCompilation: no Package: RNASeqPower Version: 1.47.0 License: LGPL (>= 2) MD5sum: 6f2c7179a3708f6443a8567b04c92a63 NeedsCompilation: no Package: RnBeads Version: 2.25.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: dec334a172fd9aa648e1eadcc41b07cb NeedsCompilation: no Package: Rnits Version: 1.41.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 65ac011aeb41bd6e6a3538aa48c9de4a NeedsCompilation: no Package: roar Version: 1.43.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: e92d2d421e1561343cc66b1136ac2965 NeedsCompilation: no Package: roastgsa Version: 1.5.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: 61d52cacb7adcf9d9ec99d90125ac5e0 NeedsCompilation: no Package: ROC Version: 1.83.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: f65d1a4b2534cba1235dde3172ba2dfe NeedsCompilation: yes Package: ROCpAI Version: 1.19.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6519a4feae05766b493b437a7c950d01 NeedsCompilation: no Package: RolDE Version: 1.11.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: 9b9d0bf581c0cfc4165d86d6bcd26aa0 NeedsCompilation: no Package: rols Version: 3.3.0 Depends: methods Imports: httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 MD5sum: aacd3dea9724f1cb0875b06ccab1e760 NeedsCompilation: no Package: ROntoTools Version: 2.35.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: ec394cb63a389cef7779b508f9ade8f4 NeedsCompilation: no Package: ropls Version: 1.39.0 Depends: R (>= 3.5.0) Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis, rmarkdown, testthat License: CeCILL MD5sum: 4d289e5493420191b812db27ce914b28 NeedsCompilation: no Package: ROSeq Version: 1.19.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 7e4fca2a827f8717c1cb9c7dd5451621 NeedsCompilation: no Package: ROTS Version: 1.35.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 0a15d44466f4d10a6324ad16d69c8a92 NeedsCompilation: yes Package: rprimer Version: 1.11.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) License: GPL-3 MD5sum: a97ca648e8ffff1a4ca43e7a979a6a77 NeedsCompilation: no Package: RProtoBufLib Version: 2.19.0 Suggests: knitr, rmarkdown License: BSD_3_clause MD5sum: 8f0335d0f6de6903b2d03a073cbb9439 NeedsCompilation: yes Package: rpx Version: 2.15.0 Depends: R (>= 3.5.0), methods Imports: BiocFileCache, jsonlite, xml2, RCurl, curl, utils Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown License: GPL-2 MD5sum: f91238814bda39318921714c95d86c0c NeedsCompilation: no Package: Rqc Version: 1.41.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 63bfd0476d416c03ea7594937c3d2dd5 NeedsCompilation: yes Package: rqt Version: 1.33.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 9b1294cd5c100666fddf564946205c66 NeedsCompilation: no Package: rqubic Version: 1.53.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: 59a86d704299c0aa8db365f120c6637b NeedsCompilation: yes Package: rRDP Version: 1.41.0 Depends: Biostrings (>= 2.26.2) Imports: rJava, utils Suggests: rRDPData, knitr, rmarkdown License: GPL-2 + file LICENSE MD5sum: 23c31bcb96d9c306c2d25e10710ffd95 NeedsCompilation: no Package: RRHO Version: 1.47.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: afeddd5993538e91afdddffe4833cbc6 NeedsCompilation: no Package: rrvgo Version: 1.19.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: d2f69ff215e2f36060a5cdb4185f159d NeedsCompilation: no Package: Rsamtools Version: 2.23.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6), R (>= 3.5.0) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 2.99.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 04b5da1e275f3e2e6697edd78a8f2ae9 NeedsCompilation: yes Package: rsbml Version: 2.65.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: 891ce47c563fb5033c04d64a6ce882e4 NeedsCompilation: yes Package: rScudo Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: fb0aeb530b3312b3d1b485b3c9f5c10e NeedsCompilation: no Package: rsemmed Version: 1.17.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 6ca8be5762f62ea6d410090d226b4422 NeedsCompilation: no Package: RSeqAn Version: 1.27.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: ff90931ef09984e6a7fb2742085eee49 NeedsCompilation: yes Package: Rsubread Version: 2.21.1 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: d6c8e5db587fe6a3d63e28a8ee35fe32 NeedsCompilation: yes Package: RSVSim Version: 1.47.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign License: LGPL-3 MD5sum: d077a175a5a9c2d40e5faf851a330845 NeedsCompilation: no Package: rSWeeP Version: 1.19.0 Depends: foreach, doParallel, parallel, Biostrings, methods, utils Imports: tools, stringi, Suggests: Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: e313ddc5e9ea4f1adf66e666eedfa1b5 NeedsCompilation: no Package: RTCA Version: 1.59.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 148b27482fa6435e9a34a6cee40bdbd9 NeedsCompilation: no Package: RTCGA Version: 1.37.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: 29b7a979de36840d494a516e147d816f NeedsCompilation: no Package: RTCGAToolbox Version: 2.37.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: 8a2cc87abf470bf7f2813e6e17df699e NeedsCompilation: no Package: RTN Version: 2.31.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: ebcaf079780459340d47c45752df3fa0 NeedsCompilation: no Package: RTNduals Version: 1.31.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c883c1a7ddb2f04ec02154efc7b6d3c1 NeedsCompilation: no Package: RTNsurvival Version: 1.31.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 9bbe8d4a04eedea402bce7ca0f3b63f9 NeedsCompilation: no Package: RTopper Version: 1.53.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 4078c0d792cb94cdada8f03f4c254d0d NeedsCompilation: no Package: Rtpca Version: 1.17.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: b3b2845f8e664bcd06dd2528fc418222 NeedsCompilation: no Package: rtracklayer Version: 1.67.0 Depends: R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: 3c266720f7edeab3457dba383e6d6a27 NeedsCompilation: yes Package: Rtreemix Version: 1.69.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: d87f0f499a0f0d4fb0a4b561ecd79408 NeedsCompilation: yes Package: rTRM Version: 1.45.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 9029f178dc4dca2ca2be81736537e9e1 NeedsCompilation: no Package: rTRMui Version: 1.45.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 8261be29e8701fd4cecb0b6fead07a2f NeedsCompilation: no Package: runibic Version: 1.29.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE MD5sum: 3bb6297d3f146fd1827d0c4743862522 NeedsCompilation: yes Package: RUVcorr Version: 1.39.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: 71c7c69f04bfe8c160f8a295abbcdb83 NeedsCompilation: no Package: RUVnormalize Version: 1.41.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 4322c131c11e0c9eb066821553c7e0c1 NeedsCompilation: no Package: RUVSeq Version: 1.41.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: c419115f4bb03e3c06fe33497e7aa8ae NeedsCompilation: no Package: Rvisdiff Version: 1.5.0 Depends: R (>= 4.3.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: 91f4e65d23330fd180eaad907f9486a5 NeedsCompilation: no Package: RVS Version: 1.29.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 2071741707b26df490c2cb738fdd824c NeedsCompilation: no Package: rWikiPathways Version: 1.27.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0ab514c1aae8ccbe3bd371efb305a7d2 NeedsCompilation: no Package: S4Arrays Version: 1.7.1 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9cd020f5465114161c34fed172e1d496 NeedsCompilation: yes Package: S4Vectors Version: 0.45.2 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.53.2) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 6aa813bf92975045e46151c5fa74b0de NeedsCompilation: yes Package: safe Version: 3.47.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 0c8ab09aca4cf66fe15fa1133cc07479 NeedsCompilation: no Package: sagenhaft Version: 1.77.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 2ff10079b2ff6cd3fd84649f68c06ab0 NeedsCompilation: no Package: SAIGEgds Version: 2.7.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.43.7), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 4aab8529d6eff7422953064aca35cf20 NeedsCompilation: yes Package: sampleClassifier Version: 1.31.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 83e50c291d4ab2de44617d8eccfab3d6 NeedsCompilation: no Package: SamSPECTRAL Version: 1.61.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 5d40547650b7b01fdcd313ba7c2a32f4 NeedsCompilation: yes Package: sangeranalyseR Version: 1.17.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: 7f682a2696f551bd26b301e5c190e362 NeedsCompilation: no Package: sangerseqR Version: 1.43.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 23890fe8f11aeea3bce8d904a614c929 NeedsCompilation: no Package: SANTA Version: 2.43.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: 46356e3b0def6b3bf686f2188e26abe8 NeedsCompilation: yes Package: SARC Version: 1.5.0 Depends: R (>= 4.3), RaggedExperiment, GenomicRanges Imports: tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments License: GPL-3 MD5sum: fa87be9e1a66c1c40d0cc98443573eb9 NeedsCompilation: no Package: sarks Version: 1.19.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: ec8b6b869c4c55806f16bae283cffbf5 NeedsCompilation: no Package: satuRn Version: 1.15.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: c538b068466c14b0f421b4a907a18d89 NeedsCompilation: no Package: SBGNview Version: 1.21.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: e80d51f565493e454e073c268e3db930 NeedsCompilation: no Package: SBMLR Version: 2.3.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: a56487b538dee1225e21dd31a3355e7a NeedsCompilation: no Package: SC3 Version: 1.35.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 5bc336f780e90a61635688a015b222a1 NeedsCompilation: yes Package: Scale4C Version: 1.29.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: feeca4ff7235ffecec6226e825efccc1 NeedsCompilation: no Package: ScaledMatrix Version: 1.15.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: ce1828b0aa19967ba5db44f3e28a5da2 NeedsCompilation: no Package: SCAN.UPC Version: 2.49.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 28452d3f033b4e90e8fc17dcfefb1a67 NeedsCompilation: no Package: scanMiR Version: 1.13.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7c15a0c7ef7e45612fa26ac6b60c9a41 NeedsCompilation: no Package: scanMiRApp Version: 1.13.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: fc63d657b2d1a08345045f3d5c62fa03 NeedsCompilation: no Package: scAnnotatR Version: 1.13.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: e462b9df07b0b2f50a12071af007c17a NeedsCompilation: no Package: SCANVIS Version: 1.21.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 6084e5a2a753e55a9132919ecf8cb73d NeedsCompilation: no Package: SCArray Version: 1.15.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.31.5) Imports: S4Vectors, utils, Matrix, SparseArray (>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: f48a81d0afe749ccdf5203c09bd59859 NeedsCompilation: yes Package: SCArray.sat Version: 1.7.0 Depends: methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: 288ad9bf606def40bb2f92ba8fb56f4b NeedsCompilation: no Package: scater Version: 1.35.0 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 MD5sum: 09a5b13a790a0c8ae4deb5fa9154bdea NeedsCompilation: no Package: scatterHatch Version: 1.13.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 7c64fffdb26739df415c44844c248892 NeedsCompilation: no Package: scBFA Version: 1.21.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: d8f6cc5045e79cced845b1bef9f3deae NeedsCompilation: no Package: SCBN Version: 1.25.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: aefc94cf587de91eeb7c5f7172e2beb2 NeedsCompilation: no Package: scBubbletree Version: 1.9.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: cbadcf538e531597a80351398a7046d9 NeedsCompilation: no Package: scCB2 Version: 1.17.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: f95ec46c474c5963b0e81da3426ae1d7 NeedsCompilation: yes Package: scClassify Version: 1.19.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 22338f860870f7ed4e4dc74d794265a3 NeedsCompilation: no Package: sccomp Version: 1.11.0 Depends: R (>= 4.2.0) Imports: instantiate (>= 0.2.3), callr, fs, stats, SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue, withr, digest Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: 9d39eb5a4cb3ef247af5222e03a0b121 NeedsCompilation: no Package: scDataviz Version: 1.17.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 87777491c89c144781e80d08c1ec3379 NeedsCompilation: no Package: scDblFinder Version: 1.21.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: 73d33039841b4526a4410773928cd80d NeedsCompilation: no Package: scDD Version: 1.31.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: da18e9ffd54ba302df3666210dfd93b6 NeedsCompilation: yes Package: scDDboost Version: 1.9.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: cd366977f81041598cd5771e8c8c31d7 NeedsCompilation: yes Package: scde Version: 2.35.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 4554a1c26ddfeb2ab117fe5c3368f14f NeedsCompilation: yes Package: scDesign3 Version: 1.5.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: 6b9a176ba9c22956d7fd65f45711ea53 NeedsCompilation: no Package: scDiagnostics Version: 1.1.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7f1c17da6149872ceb83a8bcfb876ab7 NeedsCompilation: no Package: scDotPlot Version: 1.1.0 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: 6b989d5ad3d71a1e510d4d6ba3b79030 NeedsCompilation: no Package: scds Version: 1.23.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: 1408862544c35f219290f2da5bd6c6bc NeedsCompilation: no Package: SCFA Version: 1.17.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: a425b1187a41420d936c4cdf685db605 NeedsCompilation: no Package: scFeatureFilter Version: 1.27.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 978810e068f76bc355055e1f50fc9b2e NeedsCompilation: no Package: scFeatures Version: 1.7.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: 2c6d43d9dff58491e83780ce49a5f167 NeedsCompilation: no Package: scGPS Version: 1.21.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 6d8d86cde9b2ee1ed82819967ccbf37b NeedsCompilation: yes Package: schex Version: 1.21.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 044df0cb0bbe69fe40429dd858b2238d NeedsCompilation: no Package: scHOT Version: 1.19.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 49f5b07b0f96b076772af584a8a02ce2 NeedsCompilation: no Package: scider Version: 1.5.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: f58ec649c8e2dadf2c182fac32cf39aa NeedsCompilation: no Package: scifer Version: 1.9.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, reticulate, here, utils, basilisk.utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: 6a43fd8241705a2b7a5dc8c4a66c255e NeedsCompilation: no Package: scmap Version: 1.29.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 9a8d6bb902f0fbbfd400e2b8ee5af2d0 NeedsCompilation: yes Package: scMerge Version: 1.23.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: e7a0023da7a2fbb704ed0d162d419a6c NeedsCompilation: no Package: scMET Version: 1.9.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: a833076ef534b5fe2f6aa4dd17ee2263 NeedsCompilation: yes Package: scmeth Version: 1.27.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: 7cb1722a8f19208aa152b7c7f596625c NeedsCompilation: no Package: scMitoMut Version: 1.3.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: e6a7eb05e15eda9cc536770f9deb414d NeedsCompilation: yes Package: scMultiSim Version: 1.3.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5b8532b29e531eb8ea1bbc1068baeda0 NeedsCompilation: no Package: SCnorm Version: 1.29.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 91701ccf6ba680496222e68c17368ddc NeedsCompilation: no Package: scone Version: 1.31.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 751c18d0742b04c85224ca8b4c42671f NeedsCompilation: no Package: Sconify Version: 1.27.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 3d10923ef2e5d24dfbbaa1bb70ab47b6 NeedsCompilation: no Package: SCOPE Version: 1.19.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 410561e9ddb7d42d90f04fcc30497657 NeedsCompilation: no Package: scoreInvHap Version: 1.29.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 6ac61ec8a2f2613d2bb579579d06104e NeedsCompilation: no Package: scoup Version: 1.1.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 8ba750bb0cdf2cf1061afda52f5cdabc NeedsCompilation: no Package: scp Version: 1.17.0 Depends: R (>= 4.3.0), QFeatures (>= 1.13.5) Imports: IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot License: Artistic-2.0 MD5sum: 8f7e74352660b480831a9106adc12405 NeedsCompilation: no Package: scPCA Version: 1.21.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 3b2ece9f0b747f98e32655d3daf78efd NeedsCompilation: no Package: scPipe Version: 2.7.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 080f836f46f8b1b77860aec9af40b949 NeedsCompilation: yes Package: scran Version: 1.35.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: b50399d58c2d37c06c5ac5788f8fe733 NeedsCompilation: yes Package: scrapper Version: 1.1.4 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), igraph, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, scRNAseq License: MIT + file LICENSE MD5sum: b207a8dca7ca1aa85680c337f64d7795 NeedsCompilation: yes Package: scReClassify Version: 1.13.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 2f647d2eaabd77bb0c240072065d3dc6 NeedsCompilation: no Package: scRecover Version: 1.23.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 80b84472e0274c37e7684ff512c635b1 NeedsCompilation: no Package: screenCounter Version: 1.7.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, zlibbioc, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a3c9ae7098a8f04f81c0ec54a53046ff NeedsCompilation: yes Package: ScreenR Version: 1.9.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: ca3886ae9ad5f3978ba359129d8341ee NeedsCompilation: no Package: scRepertoire Version: 2.3.0 Depends: ggplot2, R (>= 4.0) Imports: cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: d86f90b0fa91fd6d2ad84c2cbc67375b NeedsCompilation: yes Package: scRNAseqApp Version: 1.7.4 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: bafe10b67539ca99396926e1ba730757 NeedsCompilation: no Package: scruff Version: 1.25.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5afa0d01b10845165684f0755423a600 NeedsCompilation: no Package: scry Version: 1.19.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 82cc98ef235ccf53dabe0f6189b93e0c NeedsCompilation: no Package: scShapes Version: 1.13.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5b2f3c03832d37f3879b3cbf60f502cf NeedsCompilation: yes Package: scTensor Version: 2.17.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 79d13a34d33f8d6455b536946d971186 NeedsCompilation: no Package: scTGIF Version: 1.21.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: a794200679da0fe705499d3c4633d611 NeedsCompilation: no Package: scTHI Version: 1.19.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 3957fc1b46aa3af828fbf80836c9fba8 NeedsCompilation: no Package: scTreeViz Version: 1.13.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: 4e6ac436529856199dbeffdfd5d2d189 NeedsCompilation: no Package: scuttle Version: 1.17.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: f5b04790204d31085cd289d03cb2f93d NeedsCompilation: yes Package: scviR Version: 1.7.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: 28a66b85bb8f3fa4521e6f4e5779c95a NeedsCompilation: no Package: SDAMS Version: 1.27.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 562c478a75b98fe3f327b642e0c5be20 NeedsCompilation: no Package: seahtrue Version: 1.1.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1), janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>= 1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>= 0.5.6), readr (>= 2.1.5), scales (>= 1.3.0) Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 8d7556c07580ebc40e1523c38ec3d421 NeedsCompilation: no Package: sechm Version: 1.15.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: fe3f6fd9143daf225c0183d6de9b7aa4 NeedsCompilation: no Package: segmenter Version: 1.13.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: 8360274193ca52b65361b6f02c558240 NeedsCompilation: no Package: segmentSeq Version: 2.41.1 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: c10b73b9722f5fd243ad1cf8a95ed55a NeedsCompilation: no Package: selectKSigs Version: 1.19.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 550c61356561b577f67aeebeb6dc1093 NeedsCompilation: yes Package: SELEX Version: 1.39.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 5f46a821d9c2b15aee5fb216a3fdabc2 NeedsCompilation: no Package: SemDist Version: 1.41.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: f6b436acfa2ac70606e7d8a933d4ca1f NeedsCompilation: no Package: semisup Version: 1.31.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: c19663363615957ac9454466f6455c49 NeedsCompilation: no Package: seq.hotSPOT Version: 1.7.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 1247b1d404059a9076ee006810ec34cb NeedsCompilation: no Package: seq2pathway Version: 1.39.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: a938073f69a98f112e9ae0725208e9c6 NeedsCompilation: no Package: SeqArray Version: 1.47.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: bd1da5b4c84bb52286dfcadea011ce90 NeedsCompilation: yes Package: seqCAT Version: 1.29.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: da150be4ad9db80deba7f975dbb1f4c4 NeedsCompilation: no Package: seqcombo Version: 1.29.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 29bb57fcd4d81e833cff1140b87d6711 NeedsCompilation: no Package: SeqGate Version: 1.17.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 04377df3f7f609246fba239f9062e3f4 NeedsCompilation: no Package: SeqGSEA Version: 1.47.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 7b814061c3a0a89ed58ae58f949240d4 NeedsCompilation: no Package: seqLogo Version: 1.73.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 8e7af1d9bc6c80e36f3e47203be24ee2 NeedsCompilation: no Package: seqPattern Version: 1.39.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 065b4d39407d437f5f5f4640bc897a80 NeedsCompilation: no Package: seqsetvis Version: 1.27.0 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: fffa4309f8bdde137a6b4f01342214a0 NeedsCompilation: no Package: SeqSQC Version: 1.29.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 1452849542e040121d65c6518543b47f NeedsCompilation: no Package: seqTools Version: 1.41.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c24c4d4c06682e30adb4e7e8e68e50a4 NeedsCompilation: yes Package: SeqVarTools Version: 1.45.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: b9c7c7877ce8dd569f3955d70eb4327f NeedsCompilation: no Package: sesame Version: 1.25.0 Depends: R (>= 4.3.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: c8fedd3ce6984218a5d37f2c3b87d4a1 NeedsCompilation: no Package: SEtools Version: 1.21.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: ab1af374a7e8f5a154a1006c244cb769 NeedsCompilation: no Package: sevenbridges Version: 1.37.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 429379eb4b52517590bd4f634231172a NeedsCompilation: no Package: sevenC Version: 1.27.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: f12d0ee46257e854bcee6b2f72a0f1a5 NeedsCompilation: no Package: SGCP Version: 1.7.0 Depends: R (>= 4.2.0) Imports: ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle License: GPL-3 MD5sum: 3d5827493aa07ea1ebb580e3f210b77d NeedsCompilation: no Package: SGSeq Version: 1.41.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2ca6dac8c6a3f2daf36e7e520161aac7 NeedsCompilation: no Package: SharedObject Version: 1.21.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 4ba71128da2350a82321ba87216e5564 NeedsCompilation: yes Package: shiny.gosling Version: 1.3.0 Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: dc5dce6416549e37921a4d52f9385377 NeedsCompilation: no Package: shinyepico Version: 1.15.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: c1674a9ccf730dcfc90f57b82aadb430 NeedsCompilation: no Package: shinyMethyl Version: 1.43.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 0d184057a18ba5a353abf33a73a564c0 NeedsCompilation: no Package: ShortRead Version: 1.65.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: f9f54bc4872f13981aeb6aac8fceb014 NeedsCompilation: yes Package: SICtools Version: 1.37.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e1fa16720baaa4a664c2da761243b20d NeedsCompilation: yes Package: sigFeature Version: 1.25.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: 76621a4696c3605ab898e5d3e8c3cc69 NeedsCompilation: no Package: SigFuge Version: 1.45.0 Depends: R (>= 3.5.0), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 15239dd76df577d36c5fb139b40c8d80 NeedsCompilation: no Package: siggenes Version: 1.81.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 79ef511a2742356a579626b0fa3ef781 NeedsCompilation: no Package: sights Version: 1.33.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 88ffe576205054ad34274ab0ce6e87ac NeedsCompilation: no Package: signatureSearch Version: 1.21.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: aa73bd93f9f8ced2122944da404fc2fc NeedsCompilation: yes Package: signeR Version: 2.9.0 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: f13426636d125c443aef56b1c11b2c2b NeedsCompilation: yes Package: SigsPack Version: 1.21.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d6c995d1c3a199501e7407fd1c8a2f2e NeedsCompilation: no Package: sigsquared Version: 1.39.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 969d6031d4182d7acdf7db957b0c7b28 NeedsCompilation: no Package: SIM Version: 1.77.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: d3388641da50862f2f7679f211038346 NeedsCompilation: yes Package: SIMAT Version: 1.39.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 9ff628b3a07b5b04a9c697fa5238ab32 NeedsCompilation: no Package: SIMD Version: 1.25.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 86057a073f9048360ed7c703fdc36657 NeedsCompilation: yes Package: SimFFPE Version: 1.19.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 973c41b699285abed9b8be8afd7c9846 NeedsCompilation: no Package: similaRpeak Version: 1.39.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 055293d24db39fa59c1ce8ddb237ed42 NeedsCompilation: no Package: SIMLR Version: 1.33.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: e13f7b726b4e66e3c3d38e76bd5e0364 NeedsCompilation: yes Package: simona Version: 1.5.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: b4028707a6654c3481f40aa4e510674d NeedsCompilation: yes Package: simPIC Version: 1.3.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: f517575958847c5d84aed00102610578 NeedsCompilation: no Package: simpleSeg Version: 1.9.0 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: 9cec74dec8117ed31fcd419c9b16df5a NeedsCompilation: no Package: simplifyEnrichment Version: 2.1.0 Depends: R (>= 4.0.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 1ae5932059a0afe6322991afe755ed6a NeedsCompilation: no Package: sincell Version: 1.39.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 99fc53dbaa9cb5aced6c634bb0354f91 NeedsCompilation: yes Package: SingleCellAlleleExperiment Version: 1.3.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8f2ffe18b1339d3792860dbdb7299314 NeedsCompilation: no Package: SingleCellExperiment Version: 1.29.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 85ff5758fcae65fb74f9581562ea293a NeedsCompilation: no Package: SingleCellSignalR Version: 1.19.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0300a9dd57604bec47533b81ae2ddcda NeedsCompilation: no Package: singleCellTK Version: 2.15.2 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter, tidyr Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: 04200ec40b491ccd0895cd26ee8deb0c NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 2.1.0 Depends: R (>= 4.4.1) Imports: BiocGenerics, Biostrings, BSgenome, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, Matrix, parallel, patchwork, plyr, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, tidyverse, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 74f94c106d47d05e78d1b197804566c3 NeedsCompilation: no Package: SingleR Version: 2.9.1 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.21.1) LinkingTo: Rcpp, beachmat, assorthead, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: b0f150d03de52dea5802e71278f3cc6f NeedsCompilation: yes Package: singscore Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: e9c29b198a42e63996f7164215957607 NeedsCompilation: no Package: SiPSiC Version: 1.7.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 9adda7dd2b14f02bf11f1d6afe01755f NeedsCompilation: no Package: sitadela Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: f4c0bc1261f66e06b1f6880fd914ca1a NeedsCompilation: no Package: sitePath Version: 1.23.0 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: ac7e259bcb769c7e4356ea79149acfa4 NeedsCompilation: yes Package: sizepower Version: 1.77.0 Depends: stats License: LGPL MD5sum: c879d4604ceb21dc257087acb1be0708 NeedsCompilation: no Package: sketchR Version: 1.3.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE MD5sum: b608ebbd307fd2b9bbb42f9d80457fa0 NeedsCompilation: no Package: skewr Version: 1.39.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 87b97a07eaadb02ccb66b9641203b06c NeedsCompilation: no Package: slalom Version: 1.29.0 Depends: R (>= 4.0) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat License: GPL-2 MD5sum: 557dfff3a3b82fe42987791b96217610 NeedsCompilation: yes Package: slingshot Version: 2.15.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 38908959724cbd9de3a2f88ce401522d NeedsCompilation: no Package: SLqPCR Version: 1.73.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: c3be6921c898cb49024a14a1fb115b73 NeedsCompilation: no Package: SMAD Version: 1.23.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 336445097ef61aab2f372cb230df60f3 NeedsCompilation: yes Package: smartid Version: 1.3.2 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: fe28a5e585f9e568d17bf326e5d3b5e0 NeedsCompilation: no Package: SMITE Version: 1.35.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 38100371870105e480ea68dde5b61bdb NeedsCompilation: no Package: smoothclust Version: 1.3.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: edb78a4eb65fe7382f074c054b9aed07 NeedsCompilation: no Package: SNAGEE Version: 1.47.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 083aa3b4ac8d16912ea6481368ae4d99 NeedsCompilation: no Package: snapcount Version: 1.19.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 3762fb8b748da42deed55778f803d2aa NeedsCompilation: no Package: snifter Version: 1.17.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 19b8495fececeb77b9146fd6fd99f08a NeedsCompilation: no Package: snm Version: 1.55.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: bcdb31a1913dcb3914c5037bbb546208 NeedsCompilation: no Package: SNPediaR Version: 1.33.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: c3d005be6b134b56ffd3b5d31c88ae01 NeedsCompilation: no Package: SNPhood Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: a923772d4b9a033039294750edf85c3b NeedsCompilation: no Package: SNPRelate Version: 1.41.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 803cd26d54adab0f6280b48aaa46ad0a NeedsCompilation: yes Package: snpStats Version: 1.57.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: 3481fd35700bf9c478a5758808e8ed22 NeedsCompilation: yes Package: soGGi Version: 1.39.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: acc79d4ade6046652b0a9afc0d9d3474 NeedsCompilation: no Package: SomaticSignatures Version: 2.43.0 Depends: R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE MD5sum: 5fb7b437eb808e4de069b2695f7e2c5a NeedsCompilation: no Package: SpaceMarkers Version: 1.3.1 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS Enhances: BiocParallel License: MIT + file LICENSE MD5sum: 56411ef9bde270c74106bd08a46b2b28 NeedsCompilation: no Package: Spaniel Version: 1.21.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: caa1ea076f80c49871752307047730fb NeedsCompilation: no Package: SpaNorm Version: 1.1.0 Depends: R (>= 4.4) Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale License: GPL (>= 3) MD5sum: 2e7f2b25be5f4d78bca359f666ff04c7 NeedsCompilation: no Package: sparrow Version: 1.13.1 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 9a66e78a6f8887d5765117834dea7a0f NeedsCompilation: no Package: SparseArray Version: 1.7.2 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.5.11) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4a7567a6c94090693a9140f98f49f3a3 NeedsCompilation: yes Package: sparseMatrixStats Version: 1.19.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cf632a40ed06cbe93386a44d4cd2d6ca NeedsCompilation: yes Package: sparsenetgls Version: 1.25.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 255ee95a1d0ccfd3b6ca9968f9465803 NeedsCompilation: no Package: SparseSignatures Version: 2.17.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: efab10084a7684ebf4bc98feb52371d7 NeedsCompilation: no Package: spaSim Version: 1.9.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: d5a55fb013a35697d9205e21baf716cf NeedsCompilation: no Package: SpatialCPie Version: 1.23.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 36320e0455530a9b02cd5fa40e77dce4 NeedsCompilation: no Package: spatialDE Version: 1.13.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 22aeb212f74362552a65b4967bc100b5 NeedsCompilation: no Package: SpatialDecon Version: 1.17.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: ed17ef6dc24428671de58bb56b7facad NeedsCompilation: no Package: SpatialExperiment Version: 1.17.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: 0edfabf3d5dd25433d329b50efc8a82f NeedsCompilation: no Package: SpatialFeatureExperiment Version: 1.9.4 Depends: R (>= 4.2.0) Imports: Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), xml2 License: Artistic-2.0 MD5sum: 316538d362892902ed7bbd4adaf2199f NeedsCompilation: no Package: spatialHeatmap Version: 2.13.0 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 5d963677c243c68ed3daed3376988e9a NeedsCompilation: no Package: SpatialOmicsOverlay Version: 1.7.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 8136667fe9a92778c0f5c87430610c80 NeedsCompilation: no Package: spatialSimGP Version: 1.1.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 86b2b027d9461f792ee9bc85613e08de NeedsCompilation: no Package: spatzie Version: 1.13.0 Depends: R (>= 4.3) Imports: BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 MD5sum: 1ece21fd1a4f1359369a885fb7f0a76d NeedsCompilation: no Package: speckle Version: 1.7.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0655cbab431cb42f5f17dce95b818038 NeedsCompilation: no Package: specL Version: 1.41.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: db5737c6df505bebd0523c9c21cae373 NeedsCompilation: no Package: SpeCond Version: 1.61.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: c43f302920b9108aff478d626707dcdf NeedsCompilation: no Package: Spectra Version: 1.17.0 Depends: R (>= 4.0.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.37.1), methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: 12e872cdfc8418de59d969ea40705678 NeedsCompilation: no Package: SpectralTAD Version: 1.23.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: 40445c71c62bea40a71269bf8958f96e NeedsCompilation: no Package: SpectraQL Version: 1.1.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: 9995c2fa51263a6be0569ce90cc4ef1d NeedsCompilation: no Package: SPEM Version: 1.47.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 74484d4559ef0e5875bb55f569c2ee69 NeedsCompilation: no Package: SPIA Version: 2.59.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 36721cc46862a634b9651dc5f5b2fda5 NeedsCompilation: no Package: SPIAT Version: 1.9.0 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: e4b9ef873d95087098d97b962f780466 NeedsCompilation: no Package: spicyR Version: 1.19.3 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes, ggh4x, coxme, ggnewscale, lifecycle, simpleSeg Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 920abff009c524959b899a18458c87df NeedsCompilation: no Package: spikeLI Version: 2.67.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 4bc6d193f1f4eef50dea6dc6864187c1 NeedsCompilation: no Package: spiky Version: 1.13.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 26eae640a73b29c3f401ecc03c1e995e NeedsCompilation: no Package: spillR Version: 1.3.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 4a72ce740460d8087aa7370037944c6b NeedsCompilation: no Package: spkTools Version: 1.63.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 6432311dcd63686234b762091ede4ebd NeedsCompilation: no Package: splatter Version: 1.31.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave License: GPL-3 + file LICENSE MD5sum: ff50d593ad6c5a09ee541218221add79 NeedsCompilation: no Package: SpliceWiz Version: 1.9.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: 733227bf14f72740e4d82963388f7d67 NeedsCompilation: yes Package: SplicingFactory Version: 1.15.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: f09aa2b929faebe5de2e7897567e48c3 NeedsCompilation: no Package: SplicingGraphs Version: 1.47.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 7993f0431a742a208da65d9f8e135810 NeedsCompilation: no Package: SplineDV Version: 0.99.11 Depends: R (>= 3.5.0) Imports: plotly, dplyr, scuttle, methods, Biobase, BiocGenerics, S4Vectors, sparseMatrixStats, SingleCellExperiment, SummarizedExperiment, Matrix (>= 1.6.4), utils Suggests: knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2, ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0) License: GPL-2 MD5sum: 15fec493df162e89d6d9a12bd57f74ff NeedsCompilation: no Package: splineTimeR Version: 1.35.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 0797269530ae8d64453b3716a5c67792 NeedsCompilation: no Package: splots Version: 1.73.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: a0f3e1c40661fc9ad85398615a316024 NeedsCompilation: no Package: SPONGE Version: 1.29.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: 322ce39486340b36cfd4ad0de1f3ef05 NeedsCompilation: no Package: spoon Version: 1.3.1 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE MD5sum: 884997a2c0fef09186a120eb7d2b04dd NeedsCompilation: no Package: SpotClean Version: 1.9.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 1f9245363f0f932debb070e44b80bd1d NeedsCompilation: yes Package: SPOTlight Version: 1.11.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: 1fea9bbebe67f856ed0b9a2b18ad3096 NeedsCompilation: no Package: spqn Version: 1.19.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: 005fc423b98190db42eb306a909ecb3a NeedsCompilation: no Package: SQLDataFrame Version: 1.21.0 Depends: DelayedArray, S4Vectors Imports: stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI Suggests: knitr, rmarkdown, BiocStyle, testthat MD5sum: ba914ce1dbf33b80bede3c4af05ca510 NeedsCompilation: no Package: squallms Version: 1.1.0 Depends: R (>= 3.5.0) Imports: xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cd04d48df6385166f9b5ea1312bc8586 NeedsCompilation: no Package: sRACIPE Version: 1.23.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE MD5sum: 9129e965914d183b60f2281414167a77 NeedsCompilation: yes Package: sscu Version: 2.37.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 4fe0d55cd906d8f493c7f388f6703789 NeedsCompilation: no Package: sSeq Version: 1.45.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: 218fcf7e70cd8329ac7d5696875d5c12 NeedsCompilation: no Package: ssize Version: 1.81.0 Depends: gdata, xtable License: LGPL MD5sum: a48a13552dee83c5724e4ff51396c091 NeedsCompilation: no Package: sSNAPPY Version: 1.11.0 Depends: R (>= 4.3.0), ggplot2 Imports: dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 0bfe3c1b9b01530ee6727bd2af663e41 NeedsCompilation: no Package: ssPATHS Version: 1.21.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 5332d79c3cfffd45f2d4e2aa078d9c74 NeedsCompilation: no Package: ssrch Version: 1.23.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6313e44aa89edb9779716d9bf319741c NeedsCompilation: no Package: ssviz Version: 1.41.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: f4ed45f748b1d29ef34d8d7c6198f183 NeedsCompilation: no Package: StabMap Version: 1.1.0 Depends: R (>= 4.4.0), Imports: igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel Suggests: scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats License: GPL-2 MD5sum: 4552eadf29943312462045a15d149416 NeedsCompilation: no Package: stageR Version: 1.29.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: 5591ee266b9a5c904b6c1eb792df025e NeedsCompilation: no Package: standR Version: 1.11.0 Depends: R (>= 4.1) Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 3c203830787739530693d3eadf3e8814 NeedsCompilation: no Package: STATegRa Version: 1.43.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: 1fb375f51e40f44d5f3e28c6bc2a3796 NeedsCompilation: no Package: Statial Version: 1.9.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 024fde4afe64267c6487f02d1b2acb9e NeedsCompilation: no Package: statTarget Version: 1.37.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 492cfd2bb1aab20bce4fa603e3da667d NeedsCompilation: no Package: stepNorm Version: 1.79.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 8f6014ef04cd41199bb209b46b9cf7da NeedsCompilation: no Package: stJoincount Version: 1.9.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 066261eadf90643a0d80ee09f8569cec NeedsCompilation: no Package: strandCheckR Version: 1.25.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 2d8bd6ddf845cf0d91123d26ea4efcbe NeedsCompilation: no Package: Streamer Version: 1.53.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: f69f5838ce73bf5a807aca786cd8e00d NeedsCompilation: yes Package: STRINGdb Version: 2.19.0 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 11c2b3878eb64348d550a23722f2e285 NeedsCompilation: no Package: struct Version: 1.19.0 Depends: R (>= 4.0) Imports: methods,ontologyIndex, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, rols Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 MD5sum: 68c8cbf1009ecdcb9d22e6ae3739e170 NeedsCompilation: no Package: Structstrings Version: 1.23.1 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 2f1158be14cda8eb0cbb8bf8d5af0bc7 NeedsCompilation: yes Package: structToolbox Version: 1.19.0 Depends: R (>= 4.0), struct (>= 1.5.1) Imports: ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs License: GPL-3 MD5sum: 7dc714778d8d17422e19badbe2414e0d NeedsCompilation: no Package: StructuralVariantAnnotation Version: 1.23.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports: assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb, Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE MD5sum: 2ec5f64ba307776cbcfe5acface03bb2 NeedsCompilation: no Package: SubCellBarCode Version: 1.23.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 49ced08324241ad505888525cf2129bc NeedsCompilation: no Package: subSeq Version: 1.37.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: 3fb3cdd26cefae528a575f42f2ad0ffe NeedsCompilation: no Package: SUITOR Version: 1.9.0 Depends: R (>= 4.2.0) Imports: stats, utils, graphics, ggplot2, BiocParallel Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 3d80aae3578383bec661c91dbd1647d6 NeedsCompilation: yes Package: SummarizedExperiment Version: 1.37.0 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.55.2), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.51.3), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), S4Arrays (>= 1.1.1), DelayedArray (>= 0.31.12) Suggests: jsonlite, rhdf5, HDF5Array (>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: 70e1a3afd21fa145657e4414256762b7 NeedsCompilation: no Package: Summix Version: 2.13.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 364f91b3a0de91670b810ef5fe070a37 NeedsCompilation: no Package: supersigs Version: 1.15.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 MD5sum: 8336d966189af1ea71990076bd9f80f3 NeedsCompilation: no Package: surfaltr Version: 1.13.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) Suggests: knitr, rmarkdown, devtools, kableExtra License: MIT + file LICENSE MD5sum: c1dfcad3085002ae70289d8326144ade NeedsCompilation: no Package: survClust Version: 1.1.0 Depends: R (>= 3.5.0) Imports: Rcpp, MultiAssayExperiment, pdist, survival LinkingTo: Rcpp Suggests: knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel License: MIT + file LICENSE MD5sum: 27e183704a22631e2bcb8a577abc7da4 NeedsCompilation: yes Package: survcomp Version: 1.57.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: bf6a43615270ed945956518a6e8dd98e NeedsCompilation: yes Package: survtype Version: 1.23.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2f374128127c956a7bf018507f2a7578 NeedsCompilation: no Package: sva Version: 3.55.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 52dfcf2063cecc3e914553cfe9faf5e2 NeedsCompilation: yes Package: svaNUMT Version: 1.13.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 09ef8d622b09389e76c8dc98cabef187 NeedsCompilation: no Package: svaRetro Version: 1.13.0 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 69b47570ac048ed05ebcd6831606b280 NeedsCompilation: no Package: SVMDO Version: 1.7.0 Depends: R(>= 4.4), shiny (>= 1.7.4) Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>= 0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1), data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1), caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DT (>= 0.33.0), DOSE (>= 3.24.2), AnnotationDbi (>= 1.60.0), org.Hs.eg.db (>= 3.16.0), dplyr (>= 1.0.10), SummarizedExperiment (>= 1.28.0), grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) License: GPL-3 MD5sum: d16eba166422453f574113d644b3ac0e NeedsCompilation: no Package: SWATH2stats Version: 1.37.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods Suggests: testthat, knitr, rmarkdown Enhances: MSstats, PECA, aLFQ License: GPL-3 MD5sum: 6f9af9fb8174d97756d25b4a2bcf2fee NeedsCompilation: no Package: SwathXtend Version: 2.29.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: 35f27c683fcb2e77d9de3991c55632d8 NeedsCompilation: no Package: swfdr Version: 1.33.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) MD5sum: c5266935511d0c75ce95a89e57212bd9 NeedsCompilation: no Package: switchBox Version: 1.43.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 MD5sum: 1d71b2ec1e5685f710f303ee2f317114 NeedsCompilation: yes Package: switchde Version: 1.33.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) MD5sum: beca95c533f01b5ec0ffa015b76d046d NeedsCompilation: no Package: synapsis Version: 1.13.0 Depends: R (>= 4.1) Imports: EBImage, stats, utils, graphics Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle License: MIT + file LICENSE MD5sum: 7c84d0cdc93d34ca0daf1daea0018ca4 NeedsCompilation: no Package: synapter Version: 2.31.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr License: GPL-2 MD5sum: d8f6450a2a1639c7a5cb8888f57853db NeedsCompilation: no Package: synergyfinder Version: 3.15.0 Depends: R (>= 4.0.0) Imports: drc (>= 3.0-1), reshape2 (>= 1.4.4), tidyverse (>= 1.3.0), dplyr (>= 1.0.3), tidyr (>= 1.1.2), purrr (>= 0.3.4), furrr (>= 0.2.2), ggplot2 (>= 3.3.3), ggforce (>= 0.3.2), grid (>= 4.0.2), vegan (>= 2.5-7), gstat (>= 2.0-6), sp (>= 1.4-5), methods (>= 4.0.2), SpatialExtremes (>= 2.0-9), ggrepel (>= 0.9.1), kriging (>= 1.1), plotly (>= 4.9.3), stringr (>= 1.4.0), future (>= 1.21.0), mice (>= 3.13.0), lattice (>= 0.20-41), nleqslv (>= 3.3.2), stats (>= 4.0.2), graphics (>= 4.0.2), grDevices (>= 4.0.2), magrittr (>= 2.0.1), pbapply (>= 1.4-3), metR (>= 0.9.1) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: ebaeba298e4b0b3bd114073d5ae5ee45 NeedsCompilation: no Package: SynExtend Version: 1.19.0 Depends: R (>= 4.4.0), DECIPHER (>= 2.28.0) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices, RSQLite, DBI Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown License: GPL-3 MD5sum: 3f0f7c651bca2facaa218ea801c5d752 NeedsCompilation: yes Package: synlet Version: 2.7.0 Depends: R (>= 3.5.0) Imports: data.table, ggplot2, grDevices, magrittr, methods, patchwork, RankProd, RColorBrewer, stats, utils Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 MD5sum: 7908cf6433f8448ef903f19ca385de49 NeedsCompilation: no Package: SynMut Version: 1.23.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: 6028356dd37f25ad42f3869b42a928ba NeedsCompilation: no Package: syntenet Version: 1.9.0 Depends: R (>= 4.2) Imports: Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang, Biostrings, rtracklayer, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph LinkingTo: Rcpp, testthat Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2, networkD3 License: GPL-3 MD5sum: 7e75ef4b44e1d6d5cdfb420d5af7da6d NeedsCompilation: yes Package: systemPipeR Version: 2.13.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, txdbmaker, VariantAnnotation (>= 1.25.11) License: Artistic-2.0 MD5sum: ce37af5f8ac40f8b34dc5c0b0d6df1b7 NeedsCompilation: no Package: systemPipeShiny Version: 1.17.0 Depends: R (>= 4.0.0), shiny (>= 1.6.0), spsUtil (>= 0.2.2), spsComps (>= 0.3.3), drawer (>= 0.2) Imports: DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools, glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce, shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus (>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats, styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite, openssl Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone License: GPL (>= 3) MD5sum: 1e23ad0dbe1f65de0e4a037ab3b17b06 NeedsCompilation: no Package: systemPipeTools Version: 1.15.0 Imports: DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr, ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble, magrittr, DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 MD5sum: d9065495c04090382d6783f2e66d1fc6 NeedsCompilation: no Package: tadar Version: 1.5.0 Depends: GenomicRanges, ggplot2, R (>= 4.4.0) Imports: BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 4ec1094982eb3ca36ccac18a841614ec NeedsCompilation: no Package: TADCompare Version: 1.17.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE MD5sum: 32881617a9c8052ad6afc0f5aaa22646 NeedsCompilation: no Package: tanggle Version: 1.13.0 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.5), utils, methods Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown License: Artistic-2.0 MD5sum: 62a08f23ec68815dc692d6b5de693c27 NeedsCompilation: no Package: TAPseq Version: 1.19.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: 17721615c70cf3cad40c4ee3d5f04c57 NeedsCompilation: no Package: target Version: 1.21.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: a260fb3073751a5663e61588e55351df NeedsCompilation: no Package: TargetDecoy Version: 1.13.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: c0bcb1232fd8687a40b267bb604a39f8 NeedsCompilation: no Package: TargetScore Version: 1.45.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 4cfb953bb22304b943a0456d58eece7b NeedsCompilation: no Package: TargetSearch Version: 2.9.1 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) MD5sum: 2777b71dd65d1e71480fd9cf04cc1b28 NeedsCompilation: yes Package: TCC Version: 1.47.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: e8552fe4193d34ba7cad72f92188e466 NeedsCompilation: no Package: TCGAbiolinks Version: 2.35.0 Depends: R (>= 4.0) Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT License: GPL (>= 3) MD5sum: 1192d63da5a193ff69dc064c144b5b12 NeedsCompilation: no Package: TCGAutils Version: 1.27.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: c922e71030a05b4eb77aa3b6156c4774 NeedsCompilation: no Package: TCseq Version: 1.31.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: bc1f4a462a2bba10b05a9ed120145239 NeedsCompilation: no Package: TDbasedUFE Version: 1.7.0 Imports: GenomicRanges, rTensor, readr, methods, MOFAdata, tximport, tximportData, graphics, stats, utils, shiny Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1e278fe8bc4250b37bede529534aafe0 NeedsCompilation: no Package: TDbasedUFEadv Version: 1.7.0 Imports: TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods, graphics, RTCGA, stats, enrichplot, DOSE, STRINGdb, enrichR, hash, shiny Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata License: GPL-3 MD5sum: c60456738e4ccc821ecefee0d4cc93ca NeedsCompilation: no Package: TEKRABber Version: 1.11.0 Depends: R (>= 4.3) Imports: apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, GenomeInfoDb, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) License: LGPL (>= 3) MD5sum: 0cfc59ea227d7c5752a1cdcc1b9fdfce NeedsCompilation: yes Package: TENxIO Version: 1.9.2 Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment Imports: BiocBaseUtils, BiocGenerics, BiocIO, GenomeInfoDb, GenomicRanges, HDF5Array, Matrix, MatrixGenerics, methods, RCurl, readr, rhdf5, R.utils, S4Vectors, utils Suggests: BiocStyle, DropletTestFiles, ExperimentHub, knitr, RaggedExperiment (>= 1.29.5), rmarkdown, Rsamtools, tinytest License: Artistic-2.0 MD5sum: c906b6c66b90e1aa3fbb89b861f1b2e0 NeedsCompilation: no Package: tenXplore Version: 1.29.0 Depends: R (>= 4.0), shiny Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils, BiocFileCache Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4c105d6cc268c46a462d653dd79c2ec3 NeedsCompilation: no Package: TEQC Version: 4.29.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: b9618179f716d73ee969a5b22e3bad6b NeedsCompilation: no Package: ternarynet Version: 1.51.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 60d2f56af87db6806e1c378e3094611c NeedsCompilation: yes Package: terraTCGAdata Version: 1.11.0 Depends: AnVILGCP, MultiAssayExperiment Imports: AnVIL, BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5d4e8cb16d91dc7ac9acdb7fbd36038c NeedsCompilation: no Package: TFARM Version: 1.29.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 4dda7040a617252c3e9e6df3e62778fb NeedsCompilation: no Package: TFBSTools Version: 1.45.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), pwalign, BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown License: GPL-2 MD5sum: 490ce2cc1e1df4f5ee7848094a4ced99 NeedsCompilation: yes Package: TFEA.ChIP Version: 1.27.0 Depends: R (>= 3.5) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 MD5sum: 43072548f15ea8e9cd47915f2cefb674 NeedsCompilation: no Package: TFHAZ Version: 1.29.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: fae831b95472009758d8f0df44768303 NeedsCompilation: no Package: TFutils Version: 1.27.1 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomeInfoDb, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 76c534adf00082e781104d83907e42cf NeedsCompilation: no Package: tidybulk Version: 1.19.0 Depends: R (>= 4.4.0), ttservice (>= 0.3.6) Imports: tibble, readr, dplyr (>= 1.1.0), magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig License: GPL-3 MD5sum: 1adcfa18adde11c0d0a57e9b83b0df46 NeedsCompilation: no Package: tidyCoverage Version: 1.3.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, ggplot2, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ac1ea52fcc07e9744b25a63fcb83a8cb NeedsCompilation: no Package: tidyFlowCore Version: 1.1.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 97d2f37a89700f78b254def2269957ee NeedsCompilation: no Package: tidyomics Version: 1.3.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE MD5sum: bda7056bf0a22a1c3b8c87832c4b89ce NeedsCompilation: no Package: tidysbml Version: 1.1.0 Depends: R (>= 4.4.0) Imports: xml2, methods Suggests: rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>= 3.0.0) License: CC BY 4.0 MD5sum: 17d4687204a874679c479fca1cb2cf98 NeedsCompilation: no Package: tidySingleCellExperiment Version: 1.17.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly License: GPL-3 MD5sum: da509aa04643501977faf2512a7fdbf8 NeedsCompilation: no Package: tidySpatialExperiment Version: 1.3.0 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment Imports: ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, plotly, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick, tidygate (>= 1.0.13), shiny Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment License: GPL (>= 3) MD5sum: 18f9001d2c8abfb27a4e124b19af9e4b NeedsCompilation: no Package: tidySummarizedExperiment Version: 1.17.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, plotly License: GPL-3 MD5sum: 377d1b39fb4be6bdacb9e0845ad189fc NeedsCompilation: no Package: tidytof Version: 1.1.0 Depends: R (>= 4.3) Imports: doParallel, dplyr, flowCore, foreach, ggplot2, ggraph, glmnet, methods, parallel, purrr, readr, recipes, rlang, stringr, survival, tidygraph, tidyr, tidyselect, yardstick, Rcpp, tibble, stats, utils, RcppHNSW LinkingTo: Rcpp Suggests: ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist, FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown, philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment, testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling, scattermore, preprocessCore, SingleCellExperiment, Seurat, SeuratObject, embed, rsample, BiocGenerics License: MIT + file LICENSE MD5sum: eb48ada25d0f81466a915917589b6c5f NeedsCompilation: yes Package: tigre Version: 1.61.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: e7a209a121b70f5b65652618b1da6799 NeedsCompilation: yes Package: TileDBArray Version: 1.17.0 Depends: SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7) Imports: methods, tiledb, S4Vectors Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 5bda2d76099598555776f593f05525cc NeedsCompilation: no Package: tilingArray Version: 1.85.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 2df281cf6701be75f4f898bb997a1266 NeedsCompilation: yes Package: timecourse Version: 1.79.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 4328777e387a0105b8192ff81b65a2ff NeedsCompilation: no Package: timeOmics Version: 1.19.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 1c3c9cc11e7454ac5f1b0c6512c5d46d NeedsCompilation: no Package: timescape Version: 1.31.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a76b5ed82ef58f46cf63e07f1be5b07d NeedsCompilation: no Package: TIN Version: 1.39.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 30a83a5e9a677815534787511fc386af NeedsCompilation: no Package: TissueEnrich Version: 1.27.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: d427cdc0fb06d1e8ab300955a3304a78 NeedsCompilation: no Package: TitanCNA Version: 1.45.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 MD5sum: 1d8b0cee3df546fc4c7768202c9590b9 NeedsCompilation: yes Package: tkWidgets Version: 1.85.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: f4ddf5399ad2f79e05610843c21b5c25 NeedsCompilation: no Package: tLOH Version: 1.15.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 504b8c4e1c4025fbd311f6090c9bb672 NeedsCompilation: no Package: TMixClust Version: 1.29.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 6c0a537b36627863903784fc6fbbd092 NeedsCompilation: no Package: TMSig Version: 1.1.0 Depends: R (>= 4.4.0), limma Imports: circlize, ComplexHeatmap, data.table, grDevices, grid, GSEABase, Matrix, methods, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 9246ff776e87b50a42f49fc346729b68 NeedsCompilation: no Package: TnT Version: 1.29.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: 9bc4e132220369fe862332485979a3ed NeedsCompilation: no Package: TOAST Version: 1.21.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: a23c4fa1cee103bf6368d051da1df8d9 NeedsCompilation: no Package: tomoda Version: 1.17.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 435346198d6cb76c0ab1c442dfb21b81 NeedsCompilation: no Package: tomoseqr Version: 1.11.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f51a85e39fa55ea1b1977be9cd395bf0 NeedsCompilation: no Package: TOP Version: 1.7.0 Depends: R (>= 3.5.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: 1612a2158529fb5e90b70e73d1bc83cc NeedsCompilation: no Package: topconfects Version: 1.23.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: dca4ca73d49e5473fddc823bbe3c80bf NeedsCompilation: no Package: topdownr Version: 1.29.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 185c46092d0570febe79b77ae16050c7 NeedsCompilation: no Package: topGO Version: 2.59.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: fe71239bebd66d43c7edbb9dd72c6d46 NeedsCompilation: no Package: ToxicoGx Version: 2.11.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: 7001ac978542466c845a2383c7b787e0 NeedsCompilation: no Package: TPP Version: 3.35.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 58c234aafa878dd05299ddbad3ecd683 NeedsCompilation: no Package: TPP2D Version: 1.23.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 60a62e959ebeb14d5800b8a2a7e51eaf NeedsCompilation: no Package: tpSVG Version: 1.3.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 40b2c680facb6fa89ed78440215e8ffe NeedsCompilation: no Package: tracktables Version: 1.41.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: fa65b43c4730046988c281ac5924dd4e NeedsCompilation: no Package: trackViewer Version: 1.43.1 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 7b46764419bee7d60dd44006370d425a NeedsCompilation: no Package: tradeSeq Version: 1.21.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: e5074bfbbe60b343c39343ff6b3b9166 NeedsCompilation: no Package: TrajectoryGeometry Version: 1.15.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 6936b5d9f0ee35f642983270762073bb NeedsCompilation: no Package: TrajectoryUtils Version: 1.15.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 861be6e6a334fd5679cfa6d96b428f2d NeedsCompilation: no Package: transcriptogramer Version: 1.29.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4e46733f8c014de67ac385187ae98635 NeedsCompilation: no Package: transcriptR Version: 1.35.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 9dab2c49e6a659cfa78b558909e3e0dc NeedsCompilation: no Package: transformGamPoi Version: 1.13.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2eed1e011c1d8e9cecdf828726c1dd1b NeedsCompilation: yes Package: transite Version: 1.25.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: deba913508a7157de83a43cae1f1bb74 NeedsCompilation: yes Package: tRanslatome Version: 1.45.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 39c055eef59270538c2d533c8d553e01 NeedsCompilation: no Package: transmogR Version: 1.3.0 Depends: Biostrings, GenomicRanges Imports: BSgenome, dplyr, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, jsonlite, matrixStats, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation, vroom Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: d3549484aa22f1f5386f2cf81c82a15d NeedsCompilation: no Package: transomics2cytoscape Version: 1.17.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 37512f505cb8e6fea4c36e23ebce6871 NeedsCompilation: no Package: traseR Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: f2dafa6660699e3620018bce24e240e3 NeedsCompilation: no Package: TreeAndLeaf Version: 1.19.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: 8899e853745cc65569301cbc22407019 NeedsCompilation: no Package: treeclimbR Version: 1.3.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 590fc43d3ac7bba1f3986ad1d6fb4ae8 NeedsCompilation: no Package: treeio Version: 1.31.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: ded39e57431d05609228dc47c2855950 NeedsCompilation: no Package: treekoR Version: 1.15.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: e39f993b54aedb38257c56c11043a474 NeedsCompilation: no Package: TreeSummarizedExperiment Version: 2.15.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: a2fffb1e338af26fbb0e9a0f1e46a6bb NeedsCompilation: no Package: TREG Version: 1.11.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: bf6d790a2f7175356f180b0126664d8b NeedsCompilation: no Package: Trendy Version: 1.29.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 257d938733f1bfdb35775061a4fa0160 NeedsCompilation: no Package: TRESS Version: 1.13.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 4aab0f8c710dd33d1f13c335cbe75b43 NeedsCompilation: no Package: tricycle Version: 1.15.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 956ec285d4cf7351db8410fb0deefb0b NeedsCompilation: no Package: trigger Version: 1.53.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 81d8b5dcc872c3fc9ea73b3f22b8c546 NeedsCompilation: yes Package: trio Version: 3.45.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: eb07bd4adc28a307db8dc9fa771c857a NeedsCompilation: no Package: triplex Version: 1.47.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 1ffb2b76980d2326292913d628ab1f06 NeedsCompilation: yes Package: tripr Version: 1.13.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: f548589ab9bb93b86346363c236bce31 NeedsCompilation: no Package: tRNA Version: 1.25.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: f9018a13693262425de16f80242e4535 NeedsCompilation: no Package: tRNAdbImport Version: 1.25.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 40097ce34d60a04af468d70d8af48d31 NeedsCompilation: no Package: tRNAscanImport Version: 1.27.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: b73f42b07666e33324a70b30fb1b58ad NeedsCompilation: no Package: TRONCO Version: 2.39.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: de178955e77754ac3fc6ff9f50a26900 NeedsCompilation: no Package: TSAR Version: 1.5.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 0157e88a25bb052ffcb1dbbe0a174709 NeedsCompilation: no Package: TSCAN Version: 1.45.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 69e623ecb162c79af3f6db86f06c06e6 NeedsCompilation: no Package: ttgsea Version: 1.15.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 285055aa72511e4102029ff531df9b33 NeedsCompilation: no Package: TTMap Version: 1.29.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 22daaf962871e1d7b01f88eb66c398ce NeedsCompilation: no Package: TurboNorm Version: 1.55.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 065d87e0c94d41b691e44e10d5290e03 NeedsCompilation: yes Package: TVTB Version: 1.33.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 567ae04c945bc0d7d6599c24750e5a24 NeedsCompilation: no Package: tweeDEseq Version: 1.53.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 1021653b4898869fac7e47200e22c466 NeedsCompilation: yes Package: twilight Version: 1.83.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 4f1329caa618200a7b003f235dedad92 NeedsCompilation: yes Package: twoddpcr Version: 1.31.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 0e58a5c41d8f3c6db83a3b5260c39f48 NeedsCompilation: no Package: txcutr Version: 1.13.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: ded857485f2031fd3f4d4852163161f3 NeedsCompilation: no Package: txdbmaker Version: 1.3.0 Depends: BiocGenerics, S4Vectors, GenomeInfoDb (>= 1.39.9), GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: a8c1169fcfcf90d417708b798e0180c1 NeedsCompilation: no Package: tximeta Version: 1.25.0 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: 0da89c8c21edf03498b37a28f63c5f77 NeedsCompilation: no Package: tximport Version: 1.35.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 85f907c97443d37fbee475de8467a384 NeedsCompilation: no Package: UCell Version: 2.11.1 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 00919e6937bbc94a355145cd55a79592 NeedsCompilation: no Package: UCSC.utils Version: 1.3.0 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b89a3ffa673a703bb546dda8e8c99440 NeedsCompilation: no Package: Ularcirc Version: 1.25.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: a21cc2804ddf67d21f644ef8b054b030 NeedsCompilation: no Package: UMI4Cats Version: 1.17.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: 363f3d7ea72feba68401a1806672140f NeedsCompilation: no Package: uncoverappLib Version: 1.17.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: bbf6da69aab77d8b40a14546c19c01ff NeedsCompilation: no Package: UNDO Version: 1.49.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 51def95b5d9fb9dd21c5f24b3602a3d4 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.43.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: fd5fd733afba1cba93dc4704e3b27bcd NeedsCompilation: no Package: UniProt.ws Version: 2.47.1 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 67e5612afdd5c9584b9f05a8d872ebc4 NeedsCompilation: no Package: Uniquorn Version: 2.27.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: fc77181b6bbeb6753d3486b5803d4a68 NeedsCompilation: no Package: universalmotif Version: 1.25.1 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: e91fcc1ca23a5da6e3711417d7e1799d NeedsCompilation: yes Package: updateObject Version: 1.11.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6312bf740fd11a9b1637621d273556c6 NeedsCompilation: no Package: UPDhmm Version: 1.3.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE MD5sum: 9db56f22f707cda6ebc9ba5bec3950f6 NeedsCompilation: no Package: uSORT Version: 1.33.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: e6b73fdd0201a28b925b12332c02d174 NeedsCompilation: no Package: VAExprs Version: 1.13.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: cc4fe1e1499b1399710a207769e0e756 NeedsCompilation: no Package: VanillaICE Version: 1.69.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 584557cfbe222533f7377edfbe9cae2d NeedsCompilation: yes Package: VarCon Version: 1.15.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8c82e6389f456bafaf40468f4d511800 NeedsCompilation: no Package: variancePartition Version: 1.37.1 Depends: R (>= 4.3.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: b6e5a21c596e61c6f174e1afc11ac56d NeedsCompilation: no Package: VariantAnnotation Version: 1.53.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: 7c457fa8802309f88dea2b4dace263d4 NeedsCompilation: yes Package: VariantExperiment Version: 1.21.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle License: GPL-3 MD5sum: c2afba06a82dfd830eda984ddca97509 NeedsCompilation: no Package: VariantFiltering Version: 1.43.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 04b204854a60b51e6d8ba22b2ae113d4 NeedsCompilation: yes Package: VariantTools Version: 1.49.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: 04fc8c9a302c888dc3e55a4d7f376ba2 NeedsCompilation: no Package: VaSP Version: 1.19.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 076a3408200d9eb08ebe6bd2ad090678 NeedsCompilation: no Package: vbmp Version: 1.75.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: ffe0330eb972e06eb3bdcabd794ccfa0 NeedsCompilation: no Package: VCFArray Version: 1.23.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 02fd6a1339ba27cde9b5835870f372e9 NeedsCompilation: no Package: VDJdive Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 401eda6efe28d95a363d7c15d6eccc77 NeedsCompilation: yes Package: VegaMC Version: 3.45.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 8c24e7a935bb9c5e41a602053efcded8 NeedsCompilation: yes Package: velociraptor Version: 1.17.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: b283ee3a3111445827b14b4d801cdf54 NeedsCompilation: no Package: veloviz Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 31260a7b7152c5b26da7f9500e08efe2 NeedsCompilation: yes Package: VennDetail Version: 1.23.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 742a0b6661552f1d118929c590b1bfad NeedsCompilation: no Package: VERSO Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 7448adb9f4031da3fabf898c061ca7fc NeedsCompilation: no Package: vidger Version: 1.27.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: f9c2831a0bd8ba1511c7cb6677457e55 NeedsCompilation: no Package: viper Version: 1.41.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: f1b5ae441ebec13d64676e7a8ab978a6 NeedsCompilation: no Package: VisiumIO Version: 1.3.1 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: ae09e567df572f10e95eb2b7cef813c2 NeedsCompilation: no Package: vissE Version: 1.15.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 6c495062d411be4d6541cb8089fb309c NeedsCompilation: no Package: Voyager Version: 1.9.1 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 81cb8330482fffa4931d0ea2dbd4e829 NeedsCompilation: no Package: VplotR Version: 1.17.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: a118085335952c14511d6a032c3eaf2e NeedsCompilation: no Package: vsclust Version: 1.9.3 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 MD5sum: 5d874784425df56986b695178fd4d2d2 NeedsCompilation: yes Package: vsn Version: 3.75.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: e41ee936701ec65753a4efdfb182c124 NeedsCompilation: yes Package: vtpnet Version: 0.47.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 21fac43230cc46ddd7fb57c3b22c426d NeedsCompilation: no Package: vulcan Version: 1.29.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: c90bd2f5735f443085999fd5203a1334 NeedsCompilation: no Package: waddR Version: 1.21.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache (>= 2.6.0), BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: 52d98d860ddf48368adc02cb0fd32511 NeedsCompilation: yes Package: wateRmelon Version: 2.13.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 89dcfa6a01468c7ad4c1a68f6cfc62b8 NeedsCompilation: no Package: wavClusteR Version: 2.41.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: 37cf9c0ee07c28e91d2e0dbd3eb686b5 NeedsCompilation: no Package: weaver Version: 1.73.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 5bf6b6760e01d30cc35a8e63f11d8c3f NeedsCompilation: no Package: webbioc Version: 1.79.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: bd445d134d315b150a41a3eaacd523b4 NeedsCompilation: no Package: weitrix Version: 1.19.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: da901d913905515b178002a1b165bbd1 NeedsCompilation: no Package: widgetTools Version: 1.85.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 185bae757044573d842fd9c009e83acb NeedsCompilation: no Package: wiggleplotr Version: 1.31.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: a2474fb9a4fa965fd693102ada4be3a5 NeedsCompilation: no Package: wpm Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b83709c23aa91ff32e9d2d39e5bc4c24 NeedsCompilation: no Package: wppi Version: 1.15.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 52ac0c572df18ce8ac0f4af77786c6c7 NeedsCompilation: no Package: Wrench Version: 1.25.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 9892c984775e31706960cfdfe7ac9067 NeedsCompilation: no Package: xcms Version: 4.5.0 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.15.7), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2) Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: e3b0e5dd5b8e5da54b437bcc681e3b41 NeedsCompilation: yes Package: xcore Version: 1.11.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 42f4ea7eefa4180de8cd5f758e3b99a3 NeedsCompilation: no Package: XDE Version: 2.53.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: 02c7270b21333e86c4f6e02d5d2405da NeedsCompilation: yes Package: xenLite Version: 1.1.0 Depends: R (>= 4.1) Imports: SpatialExperiment, BiocFileCache, Matrix, S4Vectors, SummarizedExperiment, methods, utils, EBImage, shiny, HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr, graphics, stats Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff License: Artistic-2.0 MD5sum: 3b8fcc41591ce447ac4f935fdb80011e NeedsCompilation: no Package: Xeva Version: 1.23.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d89e0bacda7d137e4867da02ea710a06 NeedsCompilation: no Package: XINA Version: 1.25.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: db61f27579625ccde5d74a153ba1909a NeedsCompilation: no Package: xmapbridge Version: 1.65.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: f95f1854702b67c9b83e38281d795562 NeedsCompilation: no Package: XNAString Version: 1.15.0 Depends: R (>= 4.1) Imports: utils, Biostrings, pwalign, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 MD5sum: 4dab584da0b70d4e85e5ca03dfbd3df0 NeedsCompilation: yes Package: XVector Version: 0.47.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 6dd078a5274eb5764b8588d60eeefe91 NeedsCompilation: yes Package: yamss Version: 1.33.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: d625f838264b524250e24eff8a3f2855 NeedsCompilation: no Package: YAPSA Version: 1.33.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 1dcfc83f3b2ec8974ad4fda596ee6c95 NeedsCompilation: no Package: yarn Version: 1.33.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 8c744e8a6446a582b88fcca664a621e4 NeedsCompilation: no Package: zellkonverter Version: 1.17.0 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, spelling, testthat, withr License: MIT + file LICENSE MD5sum: cb5409acefdd8a9f8f811d5284b5af93 NeedsCompilation: no Package: zenith Version: 1.9.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 085d76a00fd480d14321bde5836b9ee7 NeedsCompilation: no Package: zFPKM Version: 1.29.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 7e254537dcea3e436ae0038536107b6f NeedsCompilation: no Package: zinbwave Version: 1.29.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: eb7f67aaeb71cd4efa6e0b22f10ecfd4 NeedsCompilation: no Package: zlibbioc Version: 1.53.0 Suggests: BiocStyle, knitr License: Artistic-2.0 + file LICENSE MD5sum: e7e2281813c4523f308049af00d80414 NeedsCompilation: yes Package: ZygosityPredictor Version: 1.7.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 9500368a1acb148363195eda0ad1c55b NeedsCompilation: no