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
Package: epialleleR 1.21.3
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:
epialleleR_1.21.3.tar.gz
epialleleR_1.21.3.zip(r-4.7-x86_64)epialleleR_1.21.3.zip(r-4.7-arm64)epialleleR_1.21.3.zip(r-4.6-x86_64)epialleleR_1.21.3.zip(r-4.6-arm64)epialleleR_1.21.3.zip(r-4.5-x86_64)
epialleleR_1.21.3.tgz(r-4.6-x86_64)epialleleR_1.21.3.tgz(r-4.6-arm64)epialleleR_1.21.3.tgz(r-4.5-x86_64)epialleleR_1.21.3.tgz(r-4.5-arm64)
epialleleR_1.21.3.tar.gz(r-4.7-arm64)epialleleR_1.21.3.tar.gz(r-4.7-x86_64)epialleleR_1.21.3.tar.gz(r-4.6-arm64)epialleleR_1.21.3.tar.gz(r-4.6-x86_64)
epialleleR_1.21.3.tgz(r-4.6-emscripten)
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:
On BioConductor:epialleleR-1.21.2(bioc 3.24)epialleleR-1.20.0(bioc 3.23)
dnamethylationepigeneticsmethylseqlongreadbioconductorcytosine-methylation-reportdna-methylationepialleleepimutationlong-read-sequencingnext-generation-sequencingsamtoolsshort-read-sequencingcurlbzip2xz-utilszlibcpp
Last updated from:01e8ad3b05. Checks:14 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-arm64 | NOTE | 255 | ||
| linux-devel-x86_64 | NOTE | 325 | ||
| source / vignettes | OK | 342 | ||
| linux-release-arm64 | NOTE | 219 | ||
| linux-release-x86_64 | NOTE | 301 | ||
| macos-release-arm64 | NOTE | 163 | ||
| macos-release-x86_64 | NOTE | 540 | ||
| macos-oldrel-arm64 | NOTE | 173 | ||
| macos-oldrel-x86_64 | NOTE | 421 | ||
| windows-devel-arm64 | NOTE | 384 | ||
| windows-devel-x86_64 | NOTE | 336 | ||
| windows-release-arm64 | NOTE | 304 | ||
| windows-release-x86_64 | NOTE | 330 | ||
| windows-oldrel-x86_64 | NOTE | 237 | ||
| wasm-release | OK | 172 |
Exports:callMethylationextractPatternsgenerateAmpliconReportgenerateBedEcdfgenerateBedReportgenerateCaptureReportgenerateCytosineReportgenerateMhlReportgenerateVcfReportplotPatternspreprocessBampreprocessGenomesimulateBam
Dependencies:BHBiocGenericsdata.tablegenericsGenomicRangesIRangesRcppRhtslibS4VectorsSeqinfo
The epialleleR User's Guide
Last update: 2026-01-25
Started: 2021-04-08
The epialleleR output values
Introduction | Session Info
Last update: 2026-01-18
Started: 2023-09-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| callMethylation | callMethylation |
| extractPatterns | extractPatterns |
| generateBedEcdf | generateBedEcdf |
| generateBedReport | generateAmpliconReport generateBedReport generateCaptureReport |
| generateCytosineReport | generateCytosineReport |
| generateMhlReport | generateMhlReport |
| generateVcfReport | generateVcfReport |
| plotPatterns | plotPatterns |
| preprocessBam | preprocessBam |
| preprocessGenome | preprocessGenome |
| simulateBam | simulateBam |