- Home
- Bioconductor 3.4
- Software Packages
- chipenrich
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("chipenrich")
In most cases, you don't need to download the package archive at all.
chipenrich
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chipenrich.
Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: 3.4
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], 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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("chipenrich")
Documentation
| HTML | R Script | Vignette Title |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, Enrichment, GeneSetEnrichment, Software |
| Version | 1.12.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.1.0) |
| Imports | chipenrich.data, GenomeInfoDb, GenomicRanges, grid, IRanges, lattice, latticeExtra, methods, mgcv, parallel, plyr, rms, S4Vectors, stringr |
| LinkingTo | |
| Suggests | BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | chipenrich_1.12.1.tar.gz |
| Windows Binary | chipenrich_1.12.1.zip |
| Mac OS X 10.9 (Mavericks) | chipenrich_1.12.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/chipenrich/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/chipenrich/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
