satuRn
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see satuRn.
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Bioconductor version: 3.17
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("satuRn")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 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.
| Source Package | satuRn_1.8.0.tar.gz |
| Windows Binary | satuRn_1.8.0.zip |
| macOS Binary (x86_64) | satuRn_1.8.0.tgz |
| macOS Binary (arm64) | satuRn_1.8.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |