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epialleleR

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

Fast, Epiallele-Aware Methylation Caller and Reporter


Bioconductor version: Development (3.19)

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>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("epialleleR")

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("epialleleR")
epialleleR HTML R Script
values HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.11.9
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
URL https://github.com/BBCG/epialleleR
Bug Reports https://github.com/BBCG/epialleleR/issues
See More
Suggests RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
Linking To Rcpp, BH, Rhtslib, zlibbioc
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package epialleleR_1.11.9.tar.gz
Windows Binary epialleleR_1.11.9.zip
macOS Binary (x86_64) epialleleR_1.11.9.tgz
macOS Binary (arm64) epialleleR_1.11.9.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/
Package Downloads Report Download Stats