SOMNiBUS

DOI: 10.18129/B9.bioc.SOMNiBUS  

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

Smooth modeling of bisulfite sequencing

Bioconductor version: Development (3.18)

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 Lemaçon [ctb, ctr], Simon Laurin-Lemay [ctb, ctr], My Intelligent Machines Inc. [ctr], Celia Greenwood [ths, aut]

Maintainer: Audrey Lemaçon <audrey at mims.ai>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software
Version	1.9.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 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
LinkingTo
Suggests	BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/kaiqiong/SOMNiBUS
BugReports	https://github.com/kaiqiong/SOMNiBUS/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SOMNiBUS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SOMNiBUS
Package Short Url	https://bioconductor.org/packages/SOMNiBUS/
Package Downloads Report	Download Stats