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tweeDEseq

RNA-seq data analysis using the Poisson-Tweedie family of distributions


Bioconductor version: Release (3.18)

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

Author: Dolors Pelegri-Siso [aut, cre] , Juan R. Gonzalez [aut] , Mikel Esnaola [aut], Robert Castelo [aut]

Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>

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

Installation

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


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

BiocManager::install("tweeDEseq")

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("tweeDEseq")
tweeDEseq: analysis of RNA-seq data using the Poisson-Tweedie family of distributions PDF R Script
Reference Manual PDF

Details

biocViews DNASeq, DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>= 2)
Depends R (>= 4.3.0)
Imports Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils
System Requirements
URL https://github.com/isglobal-brge/tweeDEseq/
Bug Reports https://github.com/isglobal-brge/tweeDEseq/issues
See More
Suggests tweeDEseqCountData, xtable
Linking To Rcpp
Enhances
Depends On Me
Imports Me ptmixed
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package tweeDEseq_1.48.0.tar.gz
Windows Binary tweeDEseq_1.48.0.zip
macOS Binary (x86_64) tweeDEseq_1.48.0.tgz
macOS Binary (arm64) tweeDEseq_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tweeDEseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tweeDEseq
Bioc Package Browser https://code.bioconductor.org/browse/tweeDEseq/
Package Short Url https://bioconductor.org/packages/tweeDEseq/
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