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SplicingFactory

This is the development version of SplicingFactory; for the stable release version, see SplicingFactory.

Splicing Diversity Analysis for Transcriptome Data

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews AlternativeSplicing, DifferentialSplicing, RNASeq, Software, TranscriptomeVariant, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3 + file LICENSE
Depends R (>= 4.1)
Imports SummarizedExperiment, methods, stats
Linking To
Suggests testthat, knitr, rmarkdown, ggplot2, tidyr
System Requirements
Enhances
URL https://github.com/esebesty/SplicingFactory
Bug Reports https://github.com/esebesty/SplicingFactory/issues
See More
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_1.9.0.tar.gz
Windows Binary SplicingFactory_1.9.0.zip
macOS Binary (x86_64) SplicingFactory_1.9.0.tgz
macOS Binary (arm64) SplicingFactory_1.9.0.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/
Package Downloads Report Download Stats