ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.

Bioconductor version: 2.8

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. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages

Author: Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson,Simon Lin, David Lapointe and Michael Green

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ChIPpeakAnno")

To cite this package in a publication, start R and enter:

    citation("ChIPpeakAnno")

Documentation

PDF R Script ChIPpeakAnno Vignette
PDF   Reference Manual

Details

biocViews Annotation, ChIPseq, ChIPchip
Depends biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma
Imports biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma
Suggests
System Requirements
License GPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me oneChannelGUI
Version 1.9.0
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source ChIPpeakAnno_1.9.0.tar.gz
Windows Binary ChIPpeakAnno_1.9.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary ChIPpeakAnno_1.9.0.tgz
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