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SOMNiBUS

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

Smooth modeling of bisulfite sequencing


Bioconductor version: Development (3.19)

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 mail.mcgill.ca>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SOMNiBUS")

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

Documentation

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

browseVignettes("SOMNiBUS")
Analyzing Targeted Bisulfite Sequencing data with SOMNiBUS HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software
Version 1.11.0
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
System Requirements
URL https://github.com/kaiqiong/SOMNiBUS
Bug Reports https://github.com/kaiqiong/SOMNiBUS/issues
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Suggests BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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Package Archives

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

Source Package SOMNiBUS_1.11.0.tar.gz
Windows Binary SOMNiBUS_1.11.0.zip
macOS Binary (x86_64) SOMNiBUS_1.11.0.tgz
macOS Binary (arm64) SOMNiBUS_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SOMNiBUS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SOMNiBUS
Bioc Package Browser https://code.bioconductor.org/browse/SOMNiBUS/
Package Short Url https://bioconductor.org/packages/SOMNiBUS/
Package Downloads Report Download Stats