SplicingFactory
This is the development version of SplicingFactory; for the stable release version, see SplicingFactory.
Splicing Diversity Analysis for Transcriptome Data
Bioconductor version: Development (3.24)
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("SplicingFactory")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialSplicing, RNASeq, Software, TranscriptomeVariant, Transcriptomics |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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 |
See More
| Suggests | testthat, knitr, rmarkdown, ggplot2, tidyr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | SplicingFactory_1.21.0.tar.gz |
| Windows Binary (x86_64) | SplicingFactory_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | SplicingFactory_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | SplicingFactory_1.21.0.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 |