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

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.

AuthorGuenter Klambauer
Date of publicationNone
MaintainerGuenter Klambauer <klambauer@bioinf.jku.at>
LicenseLGPL (>= 2.0)
Version1.14.0

View on Bioconductor

Functions

`[` Man page
accessors Man page
as.data.frame,DEXUSResult-method Man page
conditionSizes Man page
conditionSizes,DEXUSResult-method Man page
countsBottomly Man page
countsGilad Man page
countsLi Man page
countsMontgomery Man page
countsPickrell Man page
dexss Man page
DEXSS, Man page
dexus Man page
DEXUS, Man page
dexus.parallel Man page
`[`,DEXUSResult,character-method Man page
[,DEXUSResult,character-method Man page
DEXUSResult-class Man page
`[`,DEXUSResult,logical-method Man page
[,DEXUSResult,logical-method Man page
`[`,DEXUSResult,numeric-method Man page
[,DEXUSResult,numeric-method Man page
dispersions Man page
dispersions,DEXUSResult-method Man page
getSizeNB Man page
INI Man page
INICalls Man page
INICalls,DEXUSResult-method Man page
INI,DEXUSResult-method Man page
INIThreshold Man page
INIThreshold<- Man page
INIThreshold<-,DEXUSResult-method Man page
INIThreshold,DEXUSResult-method Man page
INIThreshold-set Man page
INIValues Man page
INIValues,DEXUSResult-method Man page
inputData Man page
inputData,DEXUSResult-method Man page
logFC Man page
logFC,DEXUSResult-method Man page
means Man page
means,DEXUSResult-method Man page
normalizeData Man page
normalizedData Man page
normalizedData,DEXUSResult-method Man page
params Man page
params,DEXUSResult-method Man page
plot Man page
plot,DEXUSResult,missing-method Man page
posteriorProbs Man page
posteriorProbs,DEXUSResult-method Man page
pvals Man page
pvals,DEXUSResult-method Man page
responsibilities Man page
responsibilities,DEXUSResult-method Man page
sampleNames Man page
sampleNames,DEXUSResult-method Man page
show,DEXUSResult-method Man page
sizeFactors Man page
sizeFactors,DEXUSResult-method Man page
sizeParameters Man page
sizeParameters,DEXUSResult-method Man page
sort Man page
sort,DEXUSResult-method Man page
transcriptNames Man page
transcriptNames,DEXUSResult-method Man page

Files

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

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