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This is the development version of epialleleR; for the stable release version, see epialleleR.

Fast, Epiallele-Aware Methylation Caller and Reporter

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

epialleleR HTML R Script
values HTML R Script
Reference Manual PDF


biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.13.2
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, data.table, Rcpp
System Requirements C++17, GNU make
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Suggests RUnit, knitr, rmarkdown, ggplot2, gridExtra
Linking To Rcpp, BH, Rhtslib
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Follow Installation instructions to use this package in your R session.

Source Package epialleleR_1.13.2.tar.gz
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macOS Binary (x86_64) epialleleR_1.13.2.tgz
macOS Binary (arm64) epialleleR_1.13.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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