RAMEN
This is the development version of RAMEN; to use it, please install the devel version of Bioconductor.
Regional Association of Methylome variability with the Exposome and geNome
Bioconductor version: Development (3.24)
RAMEN is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome and exposome data, RAMEN identifies which individual genetic (G) or environmental (E) or joint (G+E or GxE) model better explains the VML variability. This package provides estimates of genetic and environmental contribution for each VML, allowing researchers to gain insights into the complex interplay between genetics, environment and DNA methylation.
Author: Erick I. Navarro-Delgado [aut, cre]
, Keegan Korthauer [aut]
, Michael S. Kobor [aut]
, Lluís Revilla Sancho [rev]
, Ulduz Vafadarshamasbi [rev]
, The University of British Columbia [fnd]
Maintainer: Erick I. Navarro-Delgado <erick.delgado at ubc.ca>
citation("RAMEN")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("RAMEN")
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("RAMEN")| RAMEN | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, GeneticVariability, GenomeWideAssociation, MethylationArray, Microarray, Regression, SNP, Software |
| Version | 2.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.6.0) |
| Imports | doRNG, dplyr, foreach, GenomicRanges, glmnet, IRanges, matrixStats, methods, relaimpo, S4Vectors, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, stats |
| System Requirements | |
| URL | https://ropensci.github.io/RAMEN/ https://github.com/ropensci/RAMEN/ |
| Bug Reports | https://github.com/ropensci/RAMEN/issues |
See More
| Suggests | BiocStyle, knitr, magick, rmarkdown, ggplot2, tidyr, doParallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, testthat (>= 3.0.0) |
| 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 | RAMEN_2.99.4.tar.gz |
| Windows Binary (x86_64) | RAMEN_2.99.4.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | RAMEN_2.99.4.tgz |
| macOS Binary (sonoma-arm64) | RAMEN_2.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RAMEN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RAMEN |
| Bioc Package Browser | https://code.bioconductor.org/browse/RAMEN/ |
| Package Short Url | https://bioconductor.org/packages/RAMEN/ |
| Package Downloads Report | Download Stats |