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>

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 1.8.1
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, stringi, 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_1.8.1.tar.gz
Windows Binary epialleleR_1.8.1.zip
macOS Binary (x86_64) epialleleR_1.8.1.tgz
macOS Binary (arm64) epialleleR_1.8.1.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
Old Source Packages for BioC 3.17 Source Archive