MEAL

DOI: 10.18129/B9.bioc.MEAL    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MEAL.

Perform methylation analysis

Bioconductor version: 3.9

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

Author: Carlos Ruiz-Arenas [aut, cre], Juan R. Gonzalez [aut]

Maintainer: Carlos Ruiz-Arenas <carlos.ruiz at isglobal.org>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("MEAL")

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("MEAL")

 

HTML	R Script	Expression and Methylation Analysis with MEAL
HTML	R Script	Methylation Analysis with MEAL
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DNAMethylation, Microarray, Software, WholeGenome
Version	1.14.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 years)
License	Artistic-2.0
Depends	R (>= 3.2.0), Biobase, MultiDataSet
Imports	GenomicRanges, limma, DMRcate, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats
LinkingTo
Suggests	testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	MEAL_1.14.0.tar.gz
Windows Binary	MEAL_1.14.0.zip
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/MEAL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MEAL
Package Short Url	https://bioconductor.org/packages/MEAL/
Package Downloads Report	Download Stats