dexus

DOI: 10.18129/B9.bioc.dexus    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see dexus.

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

Bioconductor version: Release (3.13)

DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

Author: Guenter Klambauer

Maintainer: Guenter Klambauer <klambauer at bioinf.jku.at>

Installation

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

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

BiocManager::install("dexus")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	CellBiology, Classification, DifferentialExpression, GeneExpression, ImmunoOncology, QualityControl, RNASeq, Sequencing, Software
Version	1.32.0
In Bioconductor since	BioC 2.12 (R-3.0) (8.5 years)
License	LGPL (>= 2.0)
Depends	R (>= 2.15), methods, BiocGenerics
Imports	stats
LinkingTo
Suggests	parallel, statmod, DESeq, RColorBrewer
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Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/dexus
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dexus
Package Short Url	https://bioconductor.org/packages/dexus/
Package Downloads Report	Download Stats