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

DOI: 10.18129/B9.bioc.chipenrich    

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: Release (3.5)

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

Maintainer: Raymond G. Cavalcante <rcavalca 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

HTML R Script chipenrich_vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression, Software
Version 2.0.1
In Bioconductor since BioC 2.13 (R-3.0) (4 years)
License GPL-3
Depends R (>= 3.3.0)
Imports AnnotationDbi, BiocGenerics, chipenrich.data(>= 1.11.4), GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors, stats, stringr, utils
LinkingTo
Suggests BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package chipenrich_2.0.1.tar.gz
Windows Binary chipenrich_2.0.1.zip
Mac OS X 10.11 (El Capitan) chipenrich_2.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/chipenrich
Package Short Url http://bioconductor.org/packages/chipenrich/
Package Downloads Report Download Stats

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