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: Development (3.0)

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, Ryan Thompson, 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
Text   NEWS

Details

biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 2.13.0
In Bioconductor since BioC 2.5 (R-2.10)
License GPL (>= 2)
Depends R (>= 2.10), grid, VennDiagram, biomaRt, IRanges, Biostrings
Imports BiocGenerics(>= 0.1.0), GO.db, BSgenome, GenomicFeatures, AnnotationDbi, limma, multtest
Suggests reactome.db, BSgenome.Ecoli.NCBI.20080805, org.Hs.eg.db, gplots, RUnit
System Requirements
URL
Depends On Me ggtut, REDseq
Imports Me FunciSNP, REDseq
Suggests Me ggtut, oneChannelGUI, RIPSeeker

Package Downloads

Package Source ChIPpeakAnno_2.13.0.tar.gz
Windows Binary ChIPpeakAnno_2.13.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChIPpeakAnno_2.13.0.tgz
Mac OS X 10.9 (Mavericks)
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