satuRn
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("satuRn")Details
| Maintainer | Jeroen Gilis <jeroen.gilis@ugent.be> |
| Author | Jeroen Gilis [aut, cre], Kristoffer Vitting-Seerup [ctb], Koen Van den Berge [ctb], Lieven Clement [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/statOmics/satuRn |
| Bug Reports | https://github.com/statOmics/satuRn/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, ExperimentalDesign, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/satuRn/ |
Citation
From within R, enter citation("satuRn"):
Jeroen Gilis. satuRn: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications. doi:10.18129/B9.bioc.satuRn, R package version 1.20.0, https://bioconductor.org/packages/satuRn.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | satuRn_1.20.0.tar.gz |
| Windows binary (x86_64) | satuRn_1.20.0.zip |
| macOS binary (arm64) | satuRn_1.20.0.tgz |
| macOS binary (x86_64) | satuRn_1.20.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics
Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray
Reverse dependencies
Depends On Me (1): IsoformSwitchAnalyzeR