ChIPpeakAnno
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ChIPpeakAnno.
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Bioconductor version: 3.17
The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>
citation("ChIPpeakAnno")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPpeakAnno")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPpeakAnno")| ChIPpeakAnno Annotation Pipeline | HTML | R Script |
| ChIPpeakAnno FAQs | HTML | R Script |
| ChIPpeakAnno Quick Start | HTML | R Script |
| ChIPpeakAnno Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ChIPSeq, ChIPchip, Software |
| Version | 3.34.1 |
| In Bioconductor since | BioC 2.5 (R-2.10) (14.5 years) |
| License | GPL (>= 2) |
| 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), DBI, dplyr, ensembldb, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils |
| System Requirements | |
| URL |
See More
| 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, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi |
| Linking To | |
| Enhances | |
| Depends On Me | REDseq, vulcan |
| Imports Me | ATACseqQC, DEScan2, GUIDEseq |
| Suggests Me | chipseqDB, R3CPET, seqsetvis |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPpeakAnno_3.34.1.tar.gz |
| Windows Binary | ChIPpeakAnno_3.34.1.zip |
| macOS Binary (x86_64) | ChIPpeakAnno_3.34.1.tgz |
| macOS Binary (arm64) | ChIPpeakAnno_3.34.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPpeakAnno |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPpeakAnno |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPpeakAnno/ |
| Package Short Url | https://bioconductor.org/packages/ChIPpeakAnno/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |