coMET

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

Bioconductor version: Release (3.17)

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 lon:g 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 (version "4.3") 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")

coMET users guide	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, MotifAnnotation, RNASeq, RiboSeq, Sequencing, Software, Visualization
Version	1.32.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 years)
License	GPL (>= 2)
Depends	R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych
Imports	hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot
Linking To
Suggests	BiocStyle, knitr, RUnit, BiocGenerics, showtext
System Requirements
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_1.32.0.tar.gz
Windows Binary	coMET_1.32.0.zip
macOS Binary (x86_64)	coMET_1.32.0.tgz
macOS Binary (arm64)	coMET_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/coMET
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/coMET
Bioc Package Browser	https://code.bioconductor.org/browse/coMET/
Package Short Url	https://bioconductor.org/packages/coMET/
Package Downloads Report	Download Stats