To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")

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

ChIPseeker

 

   

This is the development version of ChIPseeker; for the stable release version, see ChIPseeker.

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Bioconductor version: Development (3.5)

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 <guangchuangyu at gmail.com> with contributions from Yun Yan, Herve Pages, Michael Kluge and Thomas Schwarzl.

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")

Documentation

HTML 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 1.11.0
In Bioconductor since BioC 2.14 (R-3.1) (2.5 years)
License Artistic-2.0
Depends R (>= 3.3.0)
Imports AnnotationDbi, BiocGenerics, boot, DOSE, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, grid, gridBase, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors(>= 0.9.25), stats, TxDb.Hsapiens.UCSC.hg19.knownGene, UpSetR, utils
LinkingTo
Suggests clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle, rmarkdown, testthat
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/ChIPseeker
BugReports https://github.com/GuangchuangYu/ChIPseeker/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ChIPseeker_1.11.0.tar.gz
Windows Binary ChIPseeker_1.11.0.zip
Mac OS X 10.9 (Mavericks) ChIPseeker_1.11.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChIPseeker
Package Short Url http://bioconductor.org/packages/ChIPseeker/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: