ramr

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Bioconductor version: Release (3.20)

ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.

Author: Oleksii Nikolaienko [aut, cre]

Maintainer: Oleksii Nikolaienko <oleksii.nikolaienko at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ramr")

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("ramr")

ramr	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, MethylationArray, Software
Version	1.14.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	Artistic-2.0
Depends	R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods
Imports	IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors
System Requirements
URL	https://github.com/BBCG/ramr
Bug Reports	https://github.com/BBCG/ramr/issues

Suggests	RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
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	ramr_1.14.0.tar.gz
Windows Binary (x86_64)	ramr_1.14.0.zip
macOS Binary (x86_64)	ramr_1.14.0.tgz
macOS Binary (arm64)	ramr_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ramr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ramr
Bioc Package Browser	https://code.bioconductor.org/browse/ramr/
Package Short Url	https://bioconductor.org/packages/ramr/
Package Downloads Report	Download Stats