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

Smooth modeling of bisulfite sequencing

Bioconductor version: Development (3.20)

This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.

Author: Kaiqiong Zhao [aut], Kathleen Klein [cre], Audrey Lema├žon [ctb, ctr], Simon Laurin-Lemay [ctb, ctr], My Intelligent Machines Inc. [ctr], Celia Greenwood [ths, aut]

Maintainer: Kathleen Klein <kathleen.klein at>

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


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 Targeted Bisulfite Sequencing data with SOMNiBUS HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr
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Source Package SOMNiBUS_1.13.0.tar.gz
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macOS Binary (x86_64) SOMNiBUS_1.13.0.tgz
macOS Binary (arm64) SOMNiBUS_1.13.0.tgz
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