tweeDEseq

This is the released version of tweeDEseq; for the devel version, see tweeDEseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-5993-3003 , Juan R. Gonzalez [aut] ORCID: 0000-0003-3267-2146 , Mikel Esnaola [aut], Robert Castelo [aut]

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

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

Dolors Pelegri-Siso, Juan R. Gonzalez, Mikel Esnaola, Robert Castelo. tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions. doi:10.18129/B9.bioc.tweeDEseq, R package version 1.58.0, https://bioconductor.org/packages/tweeDEseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeq, DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod
Version	1.58.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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

Suggests	tweeDEseqCountData, xtable
Linking To	Rcpp
Enhances
Depends On Me
Imports Me	ptmixed
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	tweeDEseq_1.58.0.tar.gz
Windows Binary (x86_64)	tweeDEseq_1.58.0.zip
macOS Binary (big-sur-x86_64)	tweeDEseq_1.58.0.tgz
macOS Binary (sonoma-arm64)	tweeDEseq_1.58.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tweeDEseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tweeDEseq
Package Short Url	https://bioconductor.org/packages/tweeDEseq/
Package Downloads Report	Download Stats