MEAL

DOI: 10.18129/B9.bioc.MEAL    

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

Perform methylation analysis

Bioconductor version: Development (3.11)

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 <carlos.ruiz at isglobal.org>, Juan R. Gonzalez <juanr.gonzalez at isglobal.org>

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

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews DNAMethylation, Microarray, Software, WholeGenome
Version 1.17.0
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
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
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/
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