epialleleR
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see epialleleR.
Fast, Epiallele-Aware Methylation Caller and Reporter
Bioconductor version: 3.18
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("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 |
| values | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, MethylSeq, Software |
| Version | 1.10.0 |
| 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_1.10.0.tar.gz |
| Windows Binary | epialleleR_1.10.0.zip (64-bit only) |
| macOS Binary (x86_64) | epialleleR_1.10.0.tgz |
| macOS Binary (arm64) | epialleleR_1.10.0.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 |