Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
Bioconductor version: Release (3.13)
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
“4.1”) and enter:
if (!requireNamespace("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")
Details
biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, MethylationArray, Software |
Version | 1.0.3 |
In Bioconductor since | BioC 3.13 (R-4.1) ( |
License | Artistic-2.0 |
Depends | R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods |
Imports | IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors |
LinkingTo | |
Suggests | RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene |
SystemRequirements | |
Enhances | |
URL | github.com/BBCG/ramr |
BugReports | github.com/BBCG/ramr/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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Installation instructions to use this
package in your R session.
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