epialleleR

DOI: 10.18129/B9.bioc.epialleleR    

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

Fast, Epiallele-Aware Methylation Reporter

Bioconductor version: Development (3.14)

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 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 "4.1") and enter:

if (!requireNamespace("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")

 

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Details

biocViews DNAMethylation, Epigenetics, MethylSeq, Software
Version 1.1.12
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1)
Imports stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi, data.table
LinkingTo Rcpp, BH, Rhtslib, zlibbioc
Suggests RUnit, knitr, rmarkdown
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_1.1.12.tar.gz
Windows Binary epialleleR_1.1.12.zip (32- & 64-bit)
macOS 10.13 (High Sierra) epialleleR_1.1.12.tgz
Source Repository git clone https://git.bioconductor.org/packages/epialleleR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epialleleR
Package Short Url https://bioconductor.org/packages/epialleleR/
Package Downloads Report Download Stats

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