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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
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Gene Set Enrichment For ChIP-seq Peak Data
Bioconductor version: Release (3.5)
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 (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 | chipenrich_vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression, Software |
| Version | 2.0.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.0) |
| Imports | AnnotationDbi, BiocGenerics, chipenrich.data(>= 1.11.4), 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 |
| 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.
| Source Package | chipenrich_2.0.1.tar.gz |
| Windows Binary | chipenrich_2.0.1.zip |
| Mac OS X 10.11 (El Capitan) | chipenrich_2.0.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/chipenrich |
| Package Short Url | http://bioconductor.org/packages/chipenrich/ |
| Package Downloads Report | Download Stats |
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