NBSplice

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see NBSplice.

Negative Binomial Models to detect Differential Splicing


Bioconductor version: 3.9

The package proposes a differential splicing evaluation method based on isoform quantification. It applies generalized linear models with negative binomial distribution to infer changes in isoform relative expression.

Author: Gabriela A. Merino and Elmer A. Fernandez

Maintainer: Gabriela Merino <merino.gabriela33 at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("NBSplice")

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("NBSplice")
NBSplice-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, ImmunoOncology, RNASeq, Regression, Software, StatisticalMethod
Version 1.2.1
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>=2)
Depends R (>= 3.5), methods
Imports edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2
System Requirements
URL http://www.bdmg.com.ar
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Suggests knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package NBSplice_1.2.1.tar.gz
Windows Binary NBSplice_1.2.1.zip
Mac OS X 10.11 (El Capitan) NBSplice_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/NBSplice
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NBSplice
Bioc Package Browser https://code.bioconductor.org/browse/NBSplice/
Package Short Url https://bioconductor.org/packages/NBSplice/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive