coMET

This package is for version 3.13 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: 3.13

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 (version "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, MotifAnnotation, RNASeq, RiboSeq, Sequencing, Software, Visualization

Version 1.24.0

In Bioconductor since BioC 3.1 (R-3.2) (9 years)

License GPL (>= 2)

Depends R (>= 3.7.0), grid, utils, biomaRt, Gviz, psych

Imports colortools, hash, grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot

System Requirements

URL http://epigen.kcl.ac.uk/comet

Suggests BiocStyle, knitr, RUnit, BiocGenerics

Linking To

Enhances

Depends On Me

Imports Me

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Build Report Build Report

Package Archives

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

Source Package coMET_1.24.0.tar.gz

Windows Binary coMET_1.24.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) coMET_1.24.0.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

Old Source Packages for BioC 3.13 Source Archive