chipenrich

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see chipenrich.

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor version: 3.14

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 "4.1") 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 2.18.0

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

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_2.18.0.tar.gz

Windows Binary chipenrich_2.18.0.zip

macOS 10.13 (High Sierra) chipenrich_2.18.0.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

Old Source Packages for BioC 3.14 Source Archive