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 (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("coMET")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0.0), grid, utils, biomaRt, Gviz, psych
Imports	colortools, hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot
LinkingTo
Suggests	BiocStyle, knitr, RUnit, BiocGenerics, showtext
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_1.28.0.tar.gz
Windows Binary	coMET_1.28.0.zip
macOS Binary (x86_64)	coMET_1.28.0.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	https://bioconductor.org/packages/coMET/
Package Downloads Report	Download Stats