SplicingFactory

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SplicingFactory.

Splicing Diversity Analysis for Transcriptome Data

Bioconductor version: 3.21

The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.

Author: Peter A. Szikora [aut], Tamas Por [aut], Endre Sebestyen [aut, cre] ORCID iD ORCID: 0000-0001-5470-2161

Maintainer: Endre Sebestyen <endre.sebestyen at gmail.com>

Citation (from within R, enter citation("SplicingFactory")):

Installation

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


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

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("SplicingFactory")

SplicingFactory HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DifferentialSplicing, RNASeq, Software, TranscriptomeVariant, Transcriptomics

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License GPL-3 + file LICENSE

Depends R (>= 4.1)

Imports SummarizedExperiment, methods, stats

System Requirements

URL https://github.com/esebesty/SplicingFactory

Bug Reports https://github.com/esebesty/SplicingFactory/issues

Suggests testthat, knitr, rmarkdown, ggplot2, tidyr

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SplicingFactory_1.16.0.tar.gz

Windows Binary (x86_64) SplicingFactory_1.16.0.zip

macOS Binary (x86_64) SplicingFactory_1.16.0.tgz

macOS Binary (arm64) SplicingFactory_1.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SplicingFactory

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SplicingFactory

Bioc Package Browser https://code.bioconductor.org/browse/SplicingFactory/

Package Short Url https://bioconductor.org/packages/SplicingFactory/

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