regsplice

DOI: 10.18129/B9.bioc.regsplice    

L1-regularization based methods for detection of differential splicing

Bioconductor version: Release (3.13)

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

Author: Lukas M. Weber [aut, cre]

Maintainer: Lukas M. Weber <lukas.weber.edu at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("regsplice")

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("regsplice")

 

HTML	R Script	regsplice workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, ExonArray, ExperimentalDesign, ImmunoOncology, Microarray, RNASeq, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.4 (R-3.3) (5 years)
License	MIT + file LICENSE
Depends
Imports	glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/lmweber/regsplice
BugReports	https://github.com/lmweber/regsplice/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	regsplice_1.18.0.tar.gz
Windows Binary	regsplice_1.18.0.zip
macOS 10.13 (High Sierra)	regsplice_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/regsplice
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/regsplice
Package Short Url	https://bioconductor.org/packages/regsplice/
Package Downloads Report	Download Stats