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

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: 2.13

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, Herve Pages, Claude Gazin, Nathan Lawson, Jianhong Ou, Simon Lin, David Lapointe and Michael Green

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPpeakAnno")

 

PDF	R Script	ChIPpeakAnno Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPchip, ChIPseq, Software
Version	2.10.0
In Bioconductor since	BioC 2.5 (R-2.10)
License	GPL (>= 2)
Depends	R (>= 2.10), grid, VennDiagram, BiocGenerics(>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma, GenomicFeatures
Imports	gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi, GenomicFeatures
Suggests	reactome.db, RUnit, BiocGenerics
System Requirements
URL
Depends On Me	ggtut, REDseq
Imports Me	FunciSNP, REDseq
Suggests Me	ggtut, oneChannelGUI, RIPSeeker

Package Archives

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

Package Source	ChIPpeakAnno_2.10.0.tar.gz
Windows Binary	ChIPpeakAnno_2.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ChIPpeakAnno_2.10.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats