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>
citation("MEAL")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, Microarray, Software, WholeGenome |
| Version | 1.14.0 |
| 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, limma, DMRcate, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.9 | Source Archive |