chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: Release (3.17)

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], Kai Wang [cre], Chris Lee [aut], Laura J. Scott [ths], Maureen A. Sartor [ths]

Maintainer: Kai Wang <wangdaha at umich.edu>

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

Installation

To install this package, start R (version "4.3") 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	2.24.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 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
Linking To
Suggests	BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	chipenrich_2.24.0.tar.gz
Windows Binary	chipenrich_2.24.0.zip (64-bit only)
macOS Binary (x86_64)	chipenrich_2.24.0.tgz
macOS Binary (arm64)	chipenrich_2.24.0.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