epialleleR
This is the development version of epialleleR; for the stable release version, see epialleleR.
Fast, Epiallele-Aware Methylation Caller and Reporter
Bioconductor version: Development (3.21)
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 and visualise methylation patterns and assess allele specificity of methylation.
Author: Oleksii Nikolaienko [aut, cre] (ORCID:
Maintainer: Oleksii Nikolaienko <oleksii.nikolaienko at gmail.com>
citation("epialleleR")):
Installation
To install this package, start R (version "4.5") 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 |
| values | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, LongRead, MethylSeq, Software |
| Version | 1.15.1 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1) |
| Imports | stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp |
| System Requirements | C++17, GNU make |
| URL | https://github.com/BBCG/epialleleR |
| Bug Reports | https://github.com/BBCG/epialleleR/issues |
See More
| Suggests | GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 |
| Linking To | Rcpp, BH, Rhtslib |
| 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_1.15.1.tar.gz |
| Windows Binary (x86_64) | epialleleR_1.15.1.zip (64-bit only) |
| macOS Binary (x86_64) | epialleleR_1.15.1.tgz |
| macOS Binary (arm64) | |
| 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 |