SplicingFactory

DOI: 10.18129/B9.bioc.SplicingFactory    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SplicingFactory.

Splicing Diversity Analysis for Transcriptome Data

Bioconductor version: 3.15

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]

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	SplicingFactory
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, DifferentialSplicing, RNASeq, Software, TranscriptomeVariant, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1)
Imports	SummarizedExperiment, methods, stats
LinkingTo
Suggests	testthat, knitr, rmarkdown, ggplot2, tidyr
SystemRequirements
Enhances
URL	https://github.com/esebesty/SplicingFactory
BugReports	https://github.com/esebesty/SplicingFactory/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	SplicingFactory_1.4.0.tar.gz
Windows Binary	SplicingFactory_1.4.0.zip
macOS Binary (x86_64)	SplicingFactory_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SplicingFactory
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SplicingFactory
Package Short Url	https://bioconductor.org/packages/SplicingFactory/
Package Downloads Report	Download Stats