MEAL

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MEAL.

Perform methylation analysis


Bioconductor version: 3.7

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>

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

Installation

To install this package, start R (version "3.5") 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

Details

biocViews DNAMethylation, Microarray, Software, WholeGenome
Version 1.10.1
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License Artistic-2.0
Depends R (>= 3.2.0), Biobase, MultiDataSet
Imports GenomicRanges, SNPassoc, limma, DMRcate, snpStats, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats
System Requirements
URL
See More
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_1.10.1.tar.gz
Windows Binary MEAL_1.10.1.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
Old Source Packages for BioC 3.7 Source Archive