Bioconductor - epialleleR

Bioconductor - epialleleR
Bioconductor 3.22
Software Packages
epialleleR
epialleleR
This is the
released
version of epialleleR; for the devel version, see
epialleleR
Fast, Epiallele-Aware Methylation Caller and Reporter
DOI:
10.18129/B9.bioc.epialleleR
Bioconductor version:
Release (3.22)
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: 0000-0002-5910-4934
Maintainer:
Oleksii Nikolaienko
Citation (from within R, enter
citation("epialleleR")
):
Installation
To install this package, start R (version "4.5") 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
PDF
NEWS
Text
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Details
biocViews
DNAMethylation
Epigenetics
LongRead
MethylSeq
Software
Version
1.18.0
In Bioconductor since
BioC 3.13 (R-4.1) (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
Bug Reports
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
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Installation
instructions to use this package in your R session.
Source Package
epialleleR_1.18.0.tar.gz
Windows Binary (x86_64)
epialleleR_1.18.0.zip
macOS Binary (x86_64)
epialleleR_1.18.0.tgz
macOS Binary (arm64)
epialleleR_1.18.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/epialleleR
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/epialleleR
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