To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 (3.3)

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: Raymond G. Cavalcante <rcavalca at umich.edu>, Chee Lee <cheelee at umich.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 1.10.0
In Bioconductor since BioC 2.13 (R-3.0) (2.5 years)
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
LinkingTo
Suggests testthat
SystemRequirements
Enhances parallel
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source chipenrich_1.10.0.tar.gz
Windows Binary chipenrich_1.10.0.zip
Mac OS X 10.9 (Mavericks) chipenrich_1.10.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/chipenrich/tree/release-3.3
Package Short Url http://bioconductor.org/packages/chipenrich/
Package Downloads Report Download Stats

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