MEAL
This is the released version of MEAL; for the devel version, see MEAL.
Perform methylation analysis
Bioconductor version: Release (3.23)
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("MEAL")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.42.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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 |
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_1.42.0.tar.gz |
| Windows Binary (x86_64) | MEAL_1.42.0.zip |
| macOS Binary (big-sur-x86_64) | MEAL_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | MEAL_1.42.0.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 |