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epialleleR

Fast, Epiallele-Aware Methylation Reporter

Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "4.3") and enter:

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

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
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi, data.table, Rcpp
Linking To Rcpp, BH, Rhtslib, zlibbioc
Suggests RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
System Requirements C++17, GNU make
Enhances
URL https://github.com/BBCG/epialleleR
Bug Reports https://github.com/BBCG/epialleleR/issues
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Build Report  

Package Archives

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

Source Package epialleleR_1.8.0.tar.gz
Windows Binary epialleleR_1.8.0.zip
macOS Binary (x86_64) epialleleR_1.8.0.tgz
macOS Binary (arm64) epialleleR_1.8.0.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/
Package Downloads Report Download Stats