To install this package, start R and enter:

## try http if https is not available
source("https://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: 3.1

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.

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 is not available
source("https://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	1.4.7
In Bioconductor since	BioC 2.14 (R-3.1) (1.5 years)
License	Artistic-2.0
Depends	R (>= 3.1.0)
Imports	BiocGenerics, boot, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, grDevices, gtools, methods, plotrix, dplyr, parallel, plyr, magrittr, RColorBrewer, rtracklayer, S4Vectors, TxDb.Hsapiens.UCSC.hg19.knownGene
LinkingTo
Suggests	clusterProfiler, DOSE, ReactomePA, org.Hs.eg.db, knitr, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/GuangchuangYu/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_1.4.7.tar.gz
Windows Binary	ChIPseeker_1.4.7.zip
Mac OS X 10.6 (Snow Leopard)	ChIPseeker_1.4.7.tgz
Mac OS X 10.9 (Mavericks)	ChIPseeker_1.4.7.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/ChIPseeker/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/ChIPseeker/
Package Downloads Report	Download Stats

Documentation »

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