SOMNiBUS

Smooth modeling of bisulfite sequencing

Bioconductor version: Release (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 Lemaçon [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")

BiocManager::install("SOMNiBUS")

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

Documentation


Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software
Version	1.13.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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

Suggests	BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	SOMNiBUS_1.13.0.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