satuRn

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

Bioconductor version: Release (3.19)

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 "4.4") 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")

satuRn - vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, ExperimentalDesign, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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

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.

Source Package	satuRn_1.12.0.tar.gz
Windows Binary (x86_64)	satuRn_1.12.0.zip
macOS Binary (x86_64)	satuRn_1.12.0.tgz
macOS Binary (arm64)	satuRn_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/satuRn
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/satuRn
Bioc Package Browser	https://code.bioconductor.org/browse/satuRn/
Package Short Url	https://bioconductor.org/packages/satuRn/
Package Downloads Report	Download Stats