chipenrich

Gene set enrichment for ChIP-seq peak data

Bioconductor version: Release (2.14)

ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

Author: Ryan P. Welch [aut, cre, cph], Chee Lee [ctb], Laura J. Scott [ths], Maureen A. Sartor [ths]

Maintainer: Ryan P. Welch <welchr at umich.edu>

To install this package, start R and enter:

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

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

    citation("chipenrich")

Documentation

PDF R Script ChIP-Enrich Vignette/Tutorial
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, Software
Version 1.2.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-3
Depends R (>= 2.15.1)
Imports chipenrich.data, methods, GenomicRanges(>= 1.10.0), IRanges(>= 1.16.0), mgcv, plyr (>= 1.7.0), lattice, latticeExtra, grid, stringr (>= 0.6), reshape
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Package Downloads

Package Source chipenrich_1.2.0.tar.gz
Windows Binary chipenrich_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) chipenrich_1.2.0.tgz
Mac OS X 10.9 (Mavericks)
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