To install this package, start R and enter:

source("http://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 (2.14)

This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

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:

source("http://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 1.0.2
In Bioconductor since BioC 2.14 (R-3.1)
License GPL-3
Depends WriteXLS, COHCAPanno
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source COHCAP_1.0.2.tar.gz
Windows Binary COHCAP_1.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) COHCAP_1.0.2.tgz
Mac OS X 10.9 (Mavericks) COHCAP_1.0.2.tgz
Browse/checkout source (username/password: readonly)
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