To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

chipenrich

Gene set enrichment for ChIP-seq peak data

Bioconductor version: Release (3.0)

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 [aut, cre], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths]

Maintainer: Ryan P. Welch <welchr at umich.edu>, Chee Lee <cheelee at umich.edu>, Raymond G. Cavalcante <rcavalca at umich.edu>

Citation (from within R, enter citation("chipenrich")):

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("chipenrich")

 

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

Details

biocViews Bioinformatics, Enrichment, GeneSetEnrichment, Software
Version 1.4.0
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), rms
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System Requirements
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Depends On Me
Imports Me
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Package Archives

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

Package Source chipenrich_1.4.0.tar.gz
Windows Binary chipenrich_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) chipenrich_1.4.0.tgz
Mac OS X 10.9 (Mavericks) chipenrich_1.4.0.tgz
Browse/checkout source (username/password: readonly)
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