chipenrich

This is the released version of chipenrich; for the devel version, see chipenrich.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: Release (3.23)

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")):

Ryan P. Welch, Chee Lee, Raymond G. Cavalcante, Chris Lee. chipenrich: Gene Set Enrichment For ChIP-seq Peak Data. doi:10.18129/B9.bioc.chipenrich, R package version 2.36.0, https://bioconductor.org/packages/chipenrich.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software
Version	2.36.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	GPL-3
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, 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
System Requirements
URL

Suggests	BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	chipenrich_2.36.0.tar.gz
Windows Binary (x86_64)	chipenrich_2.36.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	chipenrich_2.36.0.tgz
macOS Binary (sonoma-arm64)	chipenrich_2.36.0.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/
Package Downloads Report	Download Stats