chipenrich
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see chipenrich.
Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: 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("chipenrich")):
Installation
To install this package, start R (version "4.4") 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, ImmunoOncology, Regression, Software |
| Version | 2.28.0 |
| 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_2.28.0.tar.gz |
| Windows Binary (x86_64) | chipenrich_2.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | chipenrich_2.28.0.tgz |
| macOS Binary (arm64) | chipenrich_2.28.0.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 |