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

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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
Date of publication
None
Maintainer
Guenter Klambauer <klambauer@bioinf.jku.at>
License
LGPL (>= 2.0)
Version
1.14.0

View on Bioconductor

Man pages

accessors
Accessors for a "DEXUSResult".
countsBottomly
RNA-Seq data of two mice strains.
countsGilad
RNA-Seq data of humans, chimpanzees and rhesus macaques.
countsLi
RNA-Seq data of the developmental zones of maize leaves.
countsMontgomery
RNA-Seq data of 60 European HapMap individuals.
countsPickrell
RNA-Seq data of 69 Nigerian HapMap individuals.
dexss
Detection of Differential Expression in a semi-supervised...
dexus
Detection of Differential Expression in an Unsupervised...
dexus.parallel
A parallel version of DEXUS.
DEXUSResult-class
Class '"DEXUSResult"'
DEXUSResult-subset
Subsetting a "DEXUSResult".
getSizeNB
Maximum-likelihood and maximum-a-posteriori estimators for...
INI
I/NI filtering of a DEXUS result.
INIThreshold-set
Set the I/NI threshold.
normalizeData
Normalization of RNA-Seq count data.
plot
Visualization of a result of the DEXUS algorithm.
sort
Sorting a DEXUS result.

Files in this package

dexus/DESCRIPTION
dexus/NAMESPACE
dexus/R
dexus/R/AllClasses.R
dexus/R/AllGenerics.R
dexus/R/binomTest.R
dexus/R/dexss.R
dexus/R/dexus.R
dexus/R/functions.R
dexus/R/getSizeNB.R
dexus/R/methodsAccess.R
dexus/R/normalization.R
dexus/R/plot-methods.R
dexus/R/show-methods.R
dexus/build
dexus/build/vignette.rds
dexus/data
dexus/data/datalist
dexus/data/dexus.RData
dexus/inst
dexus/inst/CITATION
dexus/inst/doc
dexus/inst/doc/dexus.R
dexus/inst/doc/dexus.Rnw
dexus/inst/doc/dexus.pdf
dexus/man
dexus/man/DEXUSResult-class.Rd
dexus/man/DEXUSResult-subset.Rd
dexus/man/INI.Rd
dexus/man/INIThreshold-set.Rd
dexus/man/accessors.Rd
dexus/man/countsBottomly.Rd
dexus/man/countsGilad.Rd
dexus/man/countsLi.Rd
dexus/man/countsMontgomery.Rd
dexus/man/countsPickrell.Rd
dexus/man/dexss.Rd
dexus/man/dexus.Rd
dexus/man/dexus.parallel.Rd
dexus/man/getSizeNB.Rd
dexus/man/normalizeData.Rd
dexus/man/plot.Rd
dexus/man/sort.Rd
dexus/src
dexus/src/dexus.cpp
dexus/vignettes
dexus/vignettes/bioinf-article.txi
dexus/vignettes/bioinf-bar.png
dexus/vignettes/bioinf.cls
dexus/vignettes/dexus.Rnw
dexus/vignettes/literature.bib
dexus/vignettes/natbib.bst
dexus/vignettes/natbib.sty