coMET
This package is for version 3.11 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: 3.11
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("coMET")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, MotifAnnotation, RNASeq, RiboSeq, Sequencing, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.6.0), 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 |
See More
| Suggests | BiocStyle, knitr, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | coMET_1.20.0.tar.gz |
| Windows Binary | coMET_1.20.0.zip |
| macOS 10.13 (High Sierra) | coMET_1.20.0.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 3.11 | Source Archive |