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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("ChIPpeakAnno")
In most cases, you don't need to download the package archive at all.
ChIPpeakAnno
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see ChIPpeakAnno.
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
Bioconductor version: 2.8
The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages
Author: Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson,Simon Lin, David Lapointe and Michael Green
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
Citation (from within R,
enter citation("ChIPpeakAnno")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPpeakAnno")
| ChIPpeakAnno.pdf | ||
| Reference Manual |
Details
| biocViews | Annotation, ChIPchip, ChIPseq, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (6.5 years) |
| License | GPL (>= 2) |
| Depends | biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma |
| Imports | biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChIPpeakAnno_1.9.0.tar.gz |
| Windows Binary | ChIPpeakAnno_1.9.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ChIPpeakAnno/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/ChIPpeakAnno/ |
| Package Downloads Report | Download Stats |
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