Package: bsseq 1.49.0

Kasper Daniel Hansen

bsseq: Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Authors:Kasper Daniel Hansen [aut, cre], Peter Hickey [aut], Hervé Pagès [ctb], Aaron Lun [ctb]

bsseq_1.49.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
bsseq/json (API)
NEWS

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

Bug tracker:https://github.com/kasperdanielhansen/bsseq/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • BS.chr22 - Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.

On BioConductor:bsseq-1.49.0(bioc 3.24)bsseq-1.48.0(bioc 3.23)

dnamethylationcpp

12.58 score 38 stars 19 packages 776 scripts 2.7k downloads 38 mentions 60 exports 81 dependencies

Last updated from:5f8162d30f. Checks:12 WARNING, 2 OK. Indexed: yes.

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Exports:assayNamesassaysbinomialGoodnessOfFitBSmoothBSmooth.tstatBSseqBSseqStatBSseqTstatchrSelectBSseqcollapseBSseqcombinecombineListdata.frame2GRangesdmrFinderendend<-estimateErrorRatefindLocifindOverlapsfisherTestsgetBSseqgetCoveragegetCpGMatrixgetCpGsgetMaxLikelihoodMatrixgetMethgetStatsgrangeshasBeenSmoothedncolnroworderBSseqoverlapsAnypDatapData<-plotManyRegionsplotRegionpoissonGoodnessOfFitread.bedMethylread.bismarkread.modbam2bedread.modkitsampleNamessampleNames<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqnamesseqnames<-showstartstart<-strandstrand<-strandCollapsesubsetByOverlapsupdateObjectwidthwidth<-

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolsh5mreadHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysviridisLiteXMLXVectoryaml

Analyzing WGBS data with bsseq

Kasper Daniel Hansen

Rendered frombsseq_analysis.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2018-09-17
Started: 2017-10-17

The bsseq User's Guide

Kasper Daniel Hansen

Rendered frombsseq.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-15
Started: 2017-10-17

Readme and manuals

Help Manual

Help pageTopics
Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.BS.chr22
BSmooth, smoothing bisulfite sequence dataBSmooth
Compute t-statistics based on smoothed whole-genome bisulfite sequencing data.BSmooth.tstat
The constructor function for BSseq objects.BSseq
Class BSseqassayNames,BSseq-method assays,BSseq-method BSseq-class chrSelectBSseq collapseBSseq combine,BSseq,BSseq-method combineList getBSseq hasBeenSmoothed length,BSseq-method orderBSseq pData,BSseq-method pData<-,BSseq,data.frame-method pData<-,BSseq,DataFrame-method sampleNames,BSseq-method sampleNames<-,BSseq,ANY-method show,BSseq-method strandCollapse updateObject,BSseq-method [,BSseq-method
Deprecated functions in package 'bsseq'bsseq-deprecated
Class BSseqStatBSseqStat BSseqStat-class show,BSseqStat-method updateObject,BSseqStat-method [,BSseqStat,ANY,ANY,ANY-method [,BSseqStat-method
Class BSseqTstatBSseqTstat BSseqTstat-class show,BSseqTstat-method updateObject,BSseqTstat-method [,BSseqTstat,ANY,ANY,ANY-method [,BSseqTstat-method
Converts a data frame to a GRanges.data.frame2GRanges
Finds differentially methylated regions for whole genome bisulfite sequencing data.dmrFinder
Estimate CpG-specific error rate from BSseq object.estimateErrorRate
Find methylation loci in a genomefindLoci
Compute Fisher-tests for a BSseq objectfisherTests
Classes FWIRanges and FWGRangesdimnames,arrayRealizationSink-method end,FWGRanges-method end,FWIRanges-method end<-,FWIRanges-method findOverlaps,FWGRanges,FWGRanges-method FWGRanges-class FWIRanges-class names,FWIRanges-method names<-,FWIRanges-method seqnames,FWGRanges-method start,FWGRanges-method start,FWIRanges-method start<-,FWIRanges-method strand,FWGRanges-method width,FWGRanges-method width,FWIRanges-method width<-,FWIRanges-method
Obtain coverage for BSseq objects.getCoverage
Generate a matrix of the most likely CpG status for a multi-sample BSseq object.getCpGMatrix
Get CpG (and non-CpG) loci from a single sample BSseq object.getCpGs
Generate a matrix of the scaled likelihood of most likely CpG status for a multi-sample BSseq object.getMaxLikelihoodMatrix
Obtain methylation estimates for BSseq objects.getMeth
Obtain statistics from a BSseqTstat objectgetStats
Binomial and poisson goodness of fit statistics for BSSeq objectsbinomialGoodnessOfFit chisqGoodnessOfFit plot.chisqGoodnessOfFit poissonGoodnessOfFit print.chisqGoodnessOfFit
Class hasGRangesclass:hasGRanges end,hasGRanges-method end<-,hasGRanges-method findOverlaps,GenomicRanges,hasGRanges-method findOverlaps,hasGRanges,GenomicRanges-method findOverlaps,hasGRanges,hasGRanges-method granges,hasGRanges-method hasGRanges hasGRanges-class length,hasGRanges-method overlapsAny,GenomicRanges,hasGRanges-method overlapsAny,hasGRanges,GenomicRanges-method overlapsAny,hasGRanges,hasGRanges-method seqlengths,hasGRanges-method seqlengths<-,hasGRanges-method seqlevels,hasGRanges-method seqlevels<-,hasGRanges-method seqnames,hasGRanges-method seqnames<-,hasGRanges-method start,hasGRanges-method start<-,hasGRanges-method strand,hasGRanges-method strand<-,hasGRanges,ANY-method strand<-,hasGRanges-method subsetByOverlaps,GenomicRanges,hasGRanges-method subsetByOverlaps,hasGRanges,GenomicRanges-method subsetByOverlaps,hasGRanges,hasGRanges-method width,hasGRanges-method width<-,hasGRanges-method [,hasGRanges,ANY,ANY,ANY-method [,hasGRanges-method
Plotting BSmooth methylation estimatesplotManyRegions plotRegion
Parsing bedMethyl output from modkit pileup.read.bedMethyl
Parsing output from the Bismark alignment suite.read.bismark