satuRn

DOI: 10.18129/B9.bioc.satuRn    

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

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

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script satuRn - vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, ExperimentalDesign, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics
LinkingTo
Suggests knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray
SystemRequirements
Enhances
URL https://github.com/statOmics/satuRn
BugReports https://github.com/statOmics/satuRn/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 satuRn_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) satuRn_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/satuRn
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/satuRn
Package Short Url https://bioconductor.org/packages/satuRn/
Package Downloads Report Download Stats

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