MEAL

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MEAL.

Perform methylation analysis

Bioconductor version: 3.19

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 "4.4") and enter:


if (!require("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")

Expression and Methylation Analysis with MEAL HTML R Script

Methylation Analysis with MEAL HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Microarray, Software, WholeGenome

Version 1.34.0

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

System Requirements

URL

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_1.34.0.tar.gz

Windows Binary (x86_64) MEAL_1.34.0.zip

macOS Binary (x86_64) MEAL_1.34.0.tgz

macOS Binary (arm64) MEAL_1.34.0.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

Old Source Packages for BioC 3.19 Source Archive