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Bioconductor - SOMNiBUS (development version)

SOMNiBUS

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

Smooth modeling of bisulfite sequencing

Bioconductor version: Development (3.22)

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 "4.5") 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 1.17.0 In Bioconductor since BioC 3.13 (R-4.1) (4 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 See More 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.


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