chipenrich

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data


Bioconductor version: 3.10

ChIP-Enrich and Poly-Enrich perform 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 "3.6") 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

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

browseVignettes("chipenrich")
chipenrich_vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software
Version 2.10.0
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, MASS, 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(>= 0.23.10), stats, stringr, utils
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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_2.10.0.tar.gz
Windows Binary chipenrich_2.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chipenrich_2.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chipenrich
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chipenrich
Bioc Package Browser https://code.bioconductor.org/browse/chipenrich/
Package Short Url https://bioconductor.org/packages/chipenrich/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive