chipenrich

DOI: 10.18129/B9.bioc.chipenrich    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	chipenrich_vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software
Version	2.12.0
In Bioconductor since	BioC 2.13 (R-3.0) (7 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
LinkingTo
Suggests	BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	chipenrich_2.12.0.tar.gz
Windows Binary	chipenrich_2.12.0.zip
macOS 10.13 (High Sierra)	chipenrich_2.12.0.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