To install this package, start R and enter:

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

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

coMET

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see coMET.

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

Bioconductor version: 3.1

Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as long as the data can be translated to genomic level and for any species.

Author: Tiphaine C. Martin, Idil Yet, Pei-Chien Tsai, Jordana T. Bell

Maintainer: Tiphaine Martin <tiphaine.martin at kcl.ac.uk>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("coMET")
PDF R Script coMET users guide
PDF coMET_manual.pdf
PDF Reference Manual
Text NEWS
Text LICENSE

Details

biocViews ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, RIPSeq, RNASeq, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License GPL (>= 2)
Depends R (>= 3.1.0), grid, biomaRt, Gviz(>= 1.10.9), psych
Imports colortools, hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, ggbio, ggplot2, trackViewer
LinkingTo
Suggests knitr, RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL http://epigen.kcl.ac.uk/comet
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source coMET_1.0.0.tar.gz
Windows Binary coMET_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) coMET_1.0.0.tgz
Mac OS X 10.9 (Mavericks) coMET_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/coMET/tree/release-3.1
Package Short Url http://bioconductor.org/packages/coMET/
Package Downloads Report Download Stats

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