Bioconductor version: Release (3.6)
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. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>, Jianhong Ou <ou.jianhong at gmail.com>
Citation (from within R,
enter citation("ChIPpeakAnno")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno")
HTML | R Script | ChIPpeakAnno Annotation Pipeline |
HTML | R Script | ChIPpeakAnno FAQs |
HTML | R Script | ChIPpeakAnno Quick Start |
HTML | R Script | ChIPpeakAnno Vignette |
Reference Manual | ||
Text | NEWS |
Follow Installation instructions to use this package in your R session.
Source Package | ChIPpeakAnno_3.12.7.tar.gz |
Windows Binary | ChIPpeakAnno_3.12.7.zip |
Mac OS X 10.11 (El Capitan) | ChIPpeakAnno_3.12.7.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/ChIPpeakAnno |
Package Short Url | http://bioconductor.org/packages/ChIPpeakAnno/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.6 | Source Archive |
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