epialleleR
This is the development version of epialleleR; for the stable release version, see epialleleR.
Fast, Epiallele-Aware Methylation Reporter
Bioconductor version: Development (3.18)
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("epialleleR")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| epialleleR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, MethylSeq, Software |
| Version | 1.9.5 |
| 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 |
See More
| 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_1.9.5.tar.gz |
| Windows Binary | epialleleR_1.9.5.zip |
| macOS Binary (x86_64) | epialleleR_1.9.5.tgz |
| macOS Binary (arm64) | epialleleR_1.9.5.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 |