DOI: 10.18129/B9.bioc.ramr  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ramr.

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Bioconductor version: 3.16

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>

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biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, MethylationArray, Software
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1), GenomicRanges, parallel, doParallel, foreach, doRNG, methods
Imports IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist, matrixStats, S4Vectors
Suggests RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
URL https://github.com/BBCG/ramr
BugReports https://github.com/BBCG/ramr/issues
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Source Package ramr_1.6.0.tar.gz
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