Package: epialleleR 1.21.0

Oleksii Nikolaienko

epialleleR: Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter

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.

Authors:Oleksii Nikolaienko [aut, cre]

epialleleR_1.21.0.tar.gz
epialleleR_1.21.0.zip(r-4.7)epialleleR_1.21.0.zip(r-4.6)epialleleR_1.21.0.zip(r-4.5)
epialleleR_1.21.0.tgz(r-4.6-x86_64)epialleleR_1.21.0.tgz(r-4.6-arm64)epialleleR_1.21.0.tgz(r-4.5-x86_64)epialleleR_1.21.0.tgz(r-4.5-arm64)
epialleleR_1.21.0.tar.gz(r-4.7-arm64)epialleleR_1.21.0.tar.gz(r-4.7-x86_64)epialleleR_1.21.0.tar.gz(r-4.6-arm64)epialleleR_1.21.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epialleleR/json (API)

# Install 'epialleleR' in R:
install.packages('epialleleR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbcg/epialleler/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:epialleleR-1.21.0(bioc 3.24)epialleleR-1.20.0(bioc 3.23)

dnamethylationepigeneticsmethylseqlongreadbioconductorcytosine-methylation-reportdna-methylationepialleleepimutationlong-read-sequencingnext-generation-sequencingsamtoolsshort-read-sequencingcurlbzip2xz-utilszlibcpp

5.86 score 6 stars 6 scripts 389 downloads 13 exports 10 dependencies

Last updated from:e1fc232267. Checks:12 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE211
linux-devel-arm64NOTE263
linux-devel-x86_64NOTE303
source / vignettesOK359
linux-release-arm64NOTE277
linux-release-x86_64NOTE348
macos-release-arm64NOTE199
macos-release-x86_64NOTE290
macos-oldrel-arm64NOTE182
macos-oldrel-x86_64NOTE295
windows-develNOTE351
windows-releaseNOTE305
windows-oldrelNOTE302
wasm-releaseFAIL214

Exports:callMethylationextractPatternsgenerateAmpliconReportgenerateBedEcdfgenerateBedReportgenerateCaptureReportgenerateCytosineReportgenerateMhlReportgenerateVcfReportplotPatternspreprocessBampreprocessGenomesimulateBam

Dependencies:BHBiocGenericsdata.tablegenericsGenomicRangesIRangesRcppRhtslibS4VectorsSeqinfo

The epialleleR User's Guide
Introduction | Current Features | Processing speed | Reference-free processing | Sample data | Amplicon-based methylation NGS data | Capture-based methylation NGS data | Long-read native NGS data (adaptive sampling) | Manually creating sample BAM files | Typical workflow | Requirements | Short-read sequencing | Long-read sequencing | Reading the data | Specific considerations for long-read sequencing data: | Optional calling of cytosine methylation | Making cytosine reports | Making VEF reports for a set of genomic regions | Linearized MHL reports | Exploring DNA methylation patterns | Exploring sequence variants in epialleles | Plotting the distribution of per-read beta values | Other information | Citing the epialleleR package | The data underlying epialleleR manuscript | Our experimental studies that use the package | Session Info | References
Rendered fromepialleleR.Rmdusingknitr::rmarkdown

Last update: 2026-01-25
Started: 2021-04-08

The epialleleR output values
Introduction | Session Info
Rendered fromvalues.Rmdusingknitr::rmarkdown

Last update: 2026-01-18
Started: 2023-09-29

Readme and manuals

Help Manual

Help pageTopics
callMethylationcallMethylation
extractPatternsextractPatterns
generateBedEcdfgenerateBedEcdf
generateBedReportgenerateAmpliconReport generateBedReport generateCaptureReport
generateCytosineReportgenerateCytosineReport
generateMhlReportgenerateMhlReport
generateVcfReportgenerateVcfReport
plotPatternsplotPatterns
preprocessBampreprocessBam
preprocessGenomepreprocessGenome
simulateBamsimulateBam