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This is the development version of bsseq; for the stable release version, see bsseq.

Analyze, manage and store bisulfite sequencing data

Bioconductor version: Development (3.20)

A collection of tools for analyzing and visualizing bisulfite sequencing data.

Author: Kasper Daniel Hansen [aut, cre], Peter Hickey [aut]

Maintainer: Kasper Daniel Hansen <kasperdanielhansen at>

Citation (from within R, enter citation("bsseq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyzing WGBS data with bsseq HTML R Script
bsseq User's Guide HTML R Script
Reference Manual PDF


biocViews DNAMethylation, Software
Version 1.41.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends R (>= 4.0), methods, BiocGenerics, GenomicRanges(>= 1.41.5), SummarizedExperiment(>= 1.19.5)
Imports IRanges(>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors(>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.5.2), permute, limma, DelayedArray(>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array(>= 1.19.11), rhdf5
System Requirements
Bug Reports
See More
Suggests testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat(>= 1.5.2), batchtools
Linking To Rcpp, beachmat
Depends On Me biscuiteer, dmrseq, DSS, bsseqData
Imports Me borealis, DMRcate, methylCC, methylSig, MIRA, NanoMethViz, scmeth, SOMNiBUS
Suggests Me methrix, tissueTreg
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package bsseq_1.41.0.tar.gz
Windows Binary
macOS Binary (x86_64) bsseq_1.41.0.tgz
macOS Binary (arm64) bsseq_1.41.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats