Package: FRASER
Type: Package
Title: Find RAre Splicing Events in RNA-Seq Data
Version: 2.7.0
Date: 2025-10-24
Authors@R: c(
    person("Christian", "Mertes", role=c("aut", "cre"), 
            email="mertes@in.tum.de", comment=c(ORCID="0000-0002-1091-205X")),
    person("Ines", "Scheller", role=c("aut"), email="scheller@in.tum.de",
            comment=c(ORCID="0000-0003-4533-7857")),
    person("Karoline", "Lutz", role=c("ctb"), email="lutzk@in.tum.de"),
    person("Ata", "Jadid Ahari", role=c("ctb"), 
            comment=c(ORCID="0009-0004-1577-7733")),
    person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de",
            comment=c(ORCID="0000-0001-7916-3643")),
    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de",
            comment=c(ORCID="0000-0002-8924-8365")))
Description: Detection of rare aberrant splicing events in
        transcriptome profiles. Read count ratio expectations are
        modeled by an autoencoder to control for confounding factors in
        the data. Given these expectations, the ratios are assumed to
        follow a beta-binomial distribution with a junction specific
        dispersion. Outlier events are then identified as read-count
        ratios that deviate significantly from this distribution.
        FRASER is able to detect alternative splicing, but also intron
        retention. The package aims to support diagnostics in the field
        of rare diseases where RNA-seq is performed to identify
        aberrant splicing defects.
biocViews: RNASeq, AlternativeSplicing, Sequencing, Software, Genetics,
        Coverage
License: file LICENSE
URL: https://github.com/gagneurlab/FRASER
BugReports: https://github.com/gagneurlab/FRASER/issues
RoxygenNote: 7.3.3
Encoding: UTF-8
VignetteBuilder: knitr
Depends: BiocParallel, Rsamtools, SummarizedExperiment
Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt,
        BSgenome, cowplot, data.table, 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, RMTstat, pracma
Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer,
        SGSeq, ggbio, biovizBase, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Hsapiens.NCBI.GRCh38,
        BSgenome.Hsapiens.1000genomes.hs37d5,
        BSgenome.Hsapiens.UCSC.hg19
LinkingTo: RcppArmadillo, Rcpp
Collate: variables.R getNSetterFuns.R FRASER-package.R
        FraserDataSet-class.R AllGenerics-definitions.R AllGenerics.R
        Fraser-pipeline.R annotationOfRanges.R beta-binomial-testing.R
        calculatePSIValue.R countRNAseqData.R example_functions.R
        filterExpression.R find_encoding_dimensions.R getURLs.R
        helper-functions.R mergeExternalData.R saveHDF5Objects.R
        RcppExports.R autoencoder.R updateD.R updateE.R updateRho.R
        pvalsNzscore.R makeSimulatedDataset.R fitCorrectionMethods.R
        plotMethods.R resultAnnotations.R zzz.R
Config/pak/sysreqs: make libmagick++-dev gsfonts libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:58:54 UTC
RemoteUrl: https://github.com/bioc/FRASER
RemoteRef: HEAD
RemoteSha: ecd421cb8bf4aaad56b19984ab33f8526364a5bc
NeedsCompilation: yes
Packaged: 2025-10-30 06:44:16 UTC; root
Author: Christian Mertes [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1091-205X>),
  Ines Scheller [aut] (ORCID: <https://orcid.org/0000-0003-4533-7857>),
  Karoline Lutz [ctb],
  Ata Jadid Ahari [ctb] (ORCID: <https://orcid.org/0009-0004-1577-7733>),
  Vicente Yepez [aut] (ORCID: <https://orcid.org/0000-0001-7916-3643>),
  Julien Gagneur [aut] (ORCID: <https://orcid.org/0000-0002-8924-8365>)
Maintainer: Christian Mertes <mertes@in.tum.de>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 06:50:48 UTC; windows
Archs: x64
