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 (3.20)
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("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 | ||
NEWS | Text |
Details
biocViews | ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, ImmunoOncology, Regression, Software |
Version | 2.29.0 |
In Bioconductor since | BioC 2.13 (R-3.0) (11 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_2.29.0.tar.gz |
Windows Binary | chipenrich_2.29.0.zip (64-bit only) |
macOS Binary (x86_64) | chipenrich_2.29.0.tgz |
macOS Binary (arm64) | chipenrich_2.29.0.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 |