epialleleR

DOI: 10.18129/B9.bioc.epialleleR  

Fast, Epiallele-Aware Methylation Reporter

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	epialleleR
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Epigenetics, MethylSeq, Software
Version	1.6.1
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
LinkingTo	Rcpp, BH, Rhtslib, zlibbioc
Suggests	RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
SystemRequirements	C++17, GNU make
Enhances
URL	https://github.com/BBCG/epialleleR
BugReports	https://github.com/BBCG/epialleleR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	epialleleR_1.6.1.tar.gz
Windows Binary	epialleleR_1.6.1.zip
macOS Binary (x86_64)	epialleleR_1.6.1.tgz
macOS Binary (arm64)	epialleleR_1.6.1.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 3.16	Source Archive