ChIPpeakAnno

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

Bioconductor version: Development (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

To install this package, start R and enter:

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

Documentation

PDF

R Script

ChIPpeakAnno Vignette

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	1.7.2

Package Downloads

Package Source	ChIPpeakAnno_1.7.2.tar.gz
Windows Binary	ChIPpeakAnno_1.7.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	ChIPpeakAnno_1.7.2.tgz
Package Downloads Report	Download Stats