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.
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ChIPpeakAnno.
Bioconductor version: 2.12
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, Herve Pages, Claude Gazin, Nathan Lawson, Jianhong Ou, Simon Lin, David Lapointe and Michael Green
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
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")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPpeakAnno")
R Script | ChIPpeakAnno Vignette | |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, ChIPchip, ChIPseq, Software |
Version | 2.8.0 |
In Bioconductor since | BioC 2.5 (R-2.10) (6.5 years) |
License | GPL (>= 2) |
Depends | R (>= 2.10), grid, VennDiagram, BiocGenerics(>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma, GenomicFeatures |
Imports | gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi, GenomicFeatures |
LinkingTo | |
Suggests | reactome.db, RUnit, BiocGenerics |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | ggtut, REDseq |
Imports Me | FunciSNP, REDseq |
Suggests Me | ggtut, oneChannelGUI, RIPSeeker |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | ChIPpeakAnno_2.8.0.tar.gz |
Windows Binary | ChIPpeakAnno_2.8.0.zip |
Mac OS X 10.6 (Snow Leopard) | ChIPpeakAnno_2.8.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/ChIPpeakAnno/tree/release-2.12 |
Package Short Url | http://bioconductor.org/packages/ChIPpeakAnno/ |
Package Downloads Report | Download Stats |
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