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coMET

This is the development version of coMET; for the stable release version, see coMET.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.35.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL (>= 2)
Depends R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych
Imports hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot
System Requirements
URL http://epigen.kcl.ac.uk/comet
See More
Suggests BiocStyle, knitr, RUnit, BiocGenerics, showtext
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Build Report Build Report

Package Archives

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

Source Package coMET_1.35.0.tar.gz
Windows Binary coMET_1.35.0.zip (64-bit only)
macOS Binary (x86_64) coMET_1.35.0.tgz
macOS Binary (arm64) coMET_1.35.0.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