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