To install this package, start R and enter:

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

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

COHCAP

 

   

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Bioconductor version: Release (3.4)

This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.

Author: Charles Warden

Maintainer: Charles Warden <cwarden45 at gmail.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("COHCAP")

 

PDF R Script COHCAP Vignette
PDF   Reference Manual

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.16.0
In Bioconductor since BioC 2.14 (R-3.1) (2.5 years)
License GPL-3
Depends WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports
LinkingTo
Suggests
SystemRequirements Perl
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source COHCAP_1.16.0.tar.gz
Windows Binary COHCAP_1.16.0.zip
Mac OS X 10.9 (Mavericks) COHCAP_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/COHCAP/tree/release-3.4
Package Short Url http://bioconductor.org/packages/COHCAP/
Package Downloads Report Download Stats

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