DOI: 10.18129/B9.bioc.epialleleR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see epialleleR.

Fast, Epiallele-Aware Methylation Reporter

Bioconductor version: 3.17

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls hypermethylated epiallele frequencies at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Other functionality includes extracting methylation patterns, computing the empirical cumulative distribution function for per-read beta values, and testing the significance of the association between epiallele methylation status and base frequencies at particular genomic positions (SNPs).

Author: Oleksii Nikolaienko [aut, cre]

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

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biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.8.1
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, stringi, 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_1.8.1.tar.gz
Windows Binary epialleleR_1.8.1.zip
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Bioc Package Browser https://code.bioconductor.org/browse/epialleleR/
Package Short Url https://bioconductor.org/packages/epialleleR/
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