chipenrich

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: 3.6

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 (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("chipenrich")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression, Software

Version 2.2.0

In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)

License GPL-3

Depends R (>= 3.4.0)

Imports AnnotationDbi, BiocGenerics, chipenrich.data, 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

System Requirements

URL

Suggests BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat

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Package Archives

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

Source Package chipenrich_2.2.0.tar.gz

Windows Binary chipenrich_2.2.0.zip

Mac OS X 10.11 (El Capitan) chipenrich_2.2.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/chipenrich

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chipenrich

Package Short Url https://bioconductor.org/packages/chipenrich/

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Old Source Packages for BioC 3.6 Source Archive