coMET

DOI: 10.18129/B9.bioc.coMET    

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

Bioconductor version: Release (3.7)

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 [aut,cre], Thomas Hardiman [aut], Idil Yet [aut], Pei-Chien Tsai [aut], Jordana T. Bell [aut]

Maintainer: Tiphaine Martin <tiphaine.martin at mssm.edu>

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("http://bioc.ism.ac.jp/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   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, MotifAnnotation, RNASeq, RiboSeq, Sequencing, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 3.1 (R-3.2) (3.5 years)
License GPL (>= 2)
Depends R (>= 3.4.0), grid, utils, biomaRt, Gviz, psych
Imports colortools, hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot
LinkingTo
Suggests BiocStyle, knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL http://epigen.kcl.ac.uk/comet
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package coMET_1.12.0.tar.gz
Windows Binary coMET_1.12.0.zip
Mac OS X 10.11 (El Capitan) coMET_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/coMET
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/coMET
Package Short Url http://bioconductor.org/packages/coMET/
Package Downloads Report Download Stats

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