DOI: 10.18129/B9.bioc.bsseq    

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

Analyze, manage and store bisulfite sequencing data

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("bsseq", version = "devel")


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



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


biocViews DNAMethylation, Software
Version 1.17.2
In Bioconductor since BioC 2.11 (R-2.15) (6 years)
License Artistic-2.0
Depends R (>= 3.3), methods, BiocGenerics, GenomicRanges(>= 1.29.14), SummarizedExperiment(>= 1.9.18), parallel
Imports IRanges(>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors, R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.1.12), permute, limma, DelayedArray(>= 0.5.34), HDF5Array
Suggests RUnit, bsseqData, BiocStyle, rmarkdown, knitr
Depends On Me bsseqData, dmrseq, DSS
Imports Me MIRA, scmeth, tcgaWGBSData.hg19
Suggests Me tissueTreg
Links To Me
Build Report  

Package Archives

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

Source Package bsseq_1.17.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) bsseq_1.17.4.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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