To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")

In most cases, you don't need to download the package archive at all.

ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Bioconductor version: Release (3.0)

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Author: Guangchuang Yu

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("ChIPseeker")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPseeker")

 

PDF R Script ChIPseeker: an R package for ChIP peak Annotation, Comparison, and Visualization
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ChIPSeq, MultipleComparison, Software, Visualization
Version 1.2.0
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 3.0)
Imports BiocGenerics, AnnotationDbi, data.table, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, grDevices, gtools, methods, plotrix, plyr, RColorBrewer, rtracklayer, S4Vectors, TxDb.Hsapiens.UCSC.hg19.knownGene
Suggests clusterProfiler, ReactomePA, DOSE, GOSemSim, org.Hs.eg.db, knitr
System Requirements
URL https://github.com/GuangchuangYu/ChIPseeker
Depends On Me
Imports Me
Suggests Me DOSE, GOSemSim, ReactomePA

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source ChIPseeker_1.2.0.tar.gz
Windows Binary ChIPseeker_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChIPseeker_1.2.0.tgz
Mac OS X 10.9 (Mavericks) ChIPseeker_1.2.0.tgz
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