Welcome to the new bioconductor.org!

chipenrich

This is the development version of chipenrich; for the stable release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.27.0
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
System Requirements
URL
See More
Suggests BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package chipenrich_2.27.0.tar.gz
Windows Binary chipenrich_2.27.0.zip
macOS Binary (x86_64) chipenrich_2.27.0.tgz
macOS Binary (arm64) chipenrich_2.27.0.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