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Bioconductor - satuRn

satuRn

This is the released version of satuRn; for the devel version, see satuRn.

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Bioconductor version: Release (3.21)

satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.

Author: Jeroen Gilis [aut, cre], Kristoffer Vitting-Seerup [ctb], Koen Van den Berge [ctb], Lieven Clement [ctb]

Maintainer: Jeroen Gilis <jeroen.gilis at ugent.be>

Citation (from within R, enter citation("satuRn")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("satuRn")

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("satuRn")
Details biocViews DifferentialExpression, ExperimentalDesign, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics, Visualization Version 1.16.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License Artistic-2.0 Depends R (>= 4.1) Imports locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics System Requirements URL https://github.com/statOmics/satuRn Bug Reports https://github.com/statOmics/satuRn/issues See More Suggests knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray Linking To Enhances Depends On Me IsoformSwitchAnalyzeR 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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