ChIPpeakAnno

This package is for version 3.6 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: 3.6

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, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>, Jianhong Ou <ou.jianhong at gmail.com>

Citation (from within R, enter citation("ChIPpeakAnno")):

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, ChIPSeq, ChIPchip, Software

Version 3.12.7

In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)

License GPL (>= 2)

Depends R (>= 3.2), methods, grid, IRanges(>= 2.11.16), Biostrings, GenomicRanges(>= 1.29.14), S4Vectors(>= 0.9.25), VennDiagram

Imports BiocGenerics(>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, Rsamtools

System Requirements

URL

Suggests reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, rtracklayer, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi

Linking To

Enhances

Depends On Me REDseq, vulcan

Imports Me ATACseqQC, DChIPRep, FunciSNP, GUIDEseq, REDseq

Suggests Me oneChannelGUI, R3CPET, RIPSeeker

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ChIPpeakAnno_3.12.7.tar.gz

Windows Binary ChIPpeakAnno_3.12.7.zip

Mac OS X 10.11 (El Capitan) ChIPpeakAnno_3.12.7.tgz

Source Repository git clone https://git.bioconductor.org/packages/ChIPpeakAnno

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPpeakAnno

Package Short Url https://bioconductor.org/packages/ChIPpeakAnno/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive