DOI: 10.18129/B9.bioc.epialleleR  

Fast, Epiallele-Aware Methylation Caller and Reporter

Bioconductor version: Release (3.18)

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract methylation patterns and assess allele specificity of methylation.

Author: Oleksii Nikolaienko [aut, cre]

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

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biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, data.table, Rcpp
LinkingTo Rcpp, BH, Rhtslib, zlibbioc
Suggests RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
SystemRequirements C++17, GNU make
URL https://github.com/BBCG/epialleleR
BugReports https://github.com/BBCG/epialleleR/issues
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Source Package epialleleR_1.10.0.tar.gz
Windows Binary epialleleR_1.10.0.zip (64-bit only)
macOS Binary (x86_64) epialleleR_1.10.0.tgz
macOS Binary (arm64) epialleleR_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/epialleleR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epialleleR
Bioc Package Browser https://code.bioconductor.org/browse/epialleleR/
Package Short Url https://bioconductor.org/packages/epialleleR/
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