Package: RBedMethyl 1.1.0

Vasileios Lemonidis

RBedMethyl: Disk-backed Representation of ONT bedMethyl Files

Bioconductor-native infrastructure for handling large nanoporetech modkit bedMethyl pileup files from ONT data using HDF5Array and DelayedArray.

Authors:Vasileios Lemonidis [aut, cre, cph], Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd]

RBedMethyl_1.1.0.tar.gz
RBedMethyl_1.1.0.zip(r-4.7)RBedMethyl_1.1.0.zip(r-4.6)RBedMethyl_1.1.0.zip(r-4.5)
RBedMethyl_1.1.0.tgz(r-4.6-any)RBedMethyl_1.1.0.tgz(r-4.5-any)
RBedMethyl_1.1.0.tar.gz(r-4.7-any)RBedMethyl_1.1.0.tar.gz(r-4.6-any)
RBedMethyl_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RBedMethyl/json (API)
NEWS

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

Bug tracker:https://github.com/cmg-ua/rbedmethyl/issues

On BioConductor:RBedMethyl-1.1.0(bioc 3.24)RBedMethyl-1.0.0(bioc 3.23)

dnamethylationdifferentialmethylationepigeneticsinfrastructuredataimportsoftware

4.30 score 3 scripts 171 downloads 8 exports 82 dependencies

Last updated from:e60c5b9d21. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE196
linux-devel-x86_64OK339
source / vignettesOK275
linux-release-x86_64OK329
macos-release-arm64OK204
macos-oldrel-arm64OK137
windows-develOK214
windows-releaseOK227
windows-oldrelOK219
wasm-releaseOK149

Exports:bedMethylFieldsbetafilterByCoveragereadBedMethylsubsetBysubsetByChromosomessubsetByRegionsummarizeByRegion

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomebsseqcigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolsh5mreadHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysviridisLiteXMLXVectoryaml

ONT-scale workflows with RBedMethyl

RBedMethyl authors

Rendered fromRBedMethyl.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-02-19
Started: 2026-02-19

Readme and manuals

Help Manual

Help pageTopics
Subset rows[,RBedMethyl,ANY,missing,missing-method [,RBedMethyl,missing,missing,missing-method [,RBedMethyl-method
List retrievable bedMethyl fieldsbedMethylFields
Per-site methylation fractionbeta,RBedMethyl,missing-method beta,RBedMethyl-method
Filter by coveragefilterByCoverage filterByCoverage,RBedMethyl-method
RBedMethyl classRBedMethyl-class
Read an ONT modkit bedMethyl filereadBedMethyl
Subset by assay predicatesubsetBy subsetBy,RBedMethyl-method
Subset by chromosomessubsetByChromosomes subsetByChromosomes,RBedMethyl-method
Subset by regionsubsetByRegion subsetByRegion,RBedMethyl,character,numeric,numeric-method subsetByRegion,RBedMethyl-method
Subset by GRangessubsetByRegion,RBedMethyl,GRanges,missing,missing-method subsetByRegion,RBedMethyl,GRanges-method
Summarize by regionssummarizeByRegion summarizeByRegion,RBedMethyl-method