chipenrich
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see chipenrich.
Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: 3.7
ChIP-Enrich performs 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>
citation("chipenrich")
):
Installation
To install this package, start R (version "3.5") 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 | ||
NEWS | Text |
Details
biocViews | ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression, Software |
Version | 2.4.0 |
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, 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, 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_2.4.0.tar.gz |
Windows Binary | chipenrich_2.4.0.zip |
Mac OS X 10.11 (El Capitan) | chipenrich_2.4.0.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 |
Old Source Packages for BioC 3.7 | Source Archive |