SOMNiBUS

DOI: 10.18129/B9.bioc.SOMNiBUS    

This is the development version of SOMNiBUS; to use it, please install the devel version of Bioconductor.

Smooth modeling of bisulfite sequencing

Bioconductor version: Development (3.13)

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]

Maintainer: Kathleen Klein <kathleen.klein at mail.mcgill.ca>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software
Version 0.99.4
In Bioconductor since BioC 3.13 (R-4.1)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports graphics, Matrix, mgcv, stats, VGAM
LinkingTo
Suggests BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/kaiqiong/SOMNiBUS
BugReports https://github.com/kaiqiong/SOMNiBUS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SOMNiBUS_0.99.4.tar.gz
Windows Binary SOMNiBUS_0.99.4.zip (32- & 64-bit)
macOS 10.13 (High Sierra) SOMNiBUS_0.99.4.tgz
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

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