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MEAL

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

Perform methylation analysis

Bioconductor version: Development (3.18)

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: Xavier Escribà Montagut <xavier.escriba at isglobal.org>

Citation (from within R, enter citation("MEAL")):

Installation

To install this package, start R (version "4.3") and enter: 

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

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

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

Details

biocViews DNAMethylation, Microarray, Software, WholeGenome
Version 1.31.0
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License Artistic-2.0
Depends R (>= 3.6.0), Biobase, MultiDataSet
Imports GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats
Linking To
Suggests testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata
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Package Archives

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

Source Package MEAL_1.31.0.tar.gz
Windows Binary MEAL_1.31.0.zip (64-bit only)
macOS Binary (x86_64) MEAL_1.31.0.tgz
macOS Binary (arm64) MEAL_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MEAL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MEAL
Bioc Package Browser https://code.bioconductor.org/browse/MEAL/
Package Short Url https://bioconductor.org/packages/MEAL/
Package Downloads Report Download Stats