chipenrich

DOI: 10.18129/B9.bioc.chipenrich    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: 3.15

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: Raymond G. Cavalcante <rcavalca at umich.edu>

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script chipenrich_vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software
Version 2.20.0
In Bioconductor since BioC 2.13 (R-3.0) (9 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_2.20.0.tar.gz
Windows Binary chipenrich_2.20.0.zip
macOS Binary (x86_64) chipenrich_2.20.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: