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

## Documentation for package ‘dexus’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

accessors | Accessors for a "DEXUSResult".
as.data.frame-method | Class '"DEXUSResult"'
conditionSizes | Accessors for a "DEXUSResult".
conditionSizes-method | Class '"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 Setting
DEXSS, | Detection of Differential Expression in a semi-supervised Setting
dexus | Detection of Differential Expression in an Unsupervised Setting
DEXUS, | Detection of Differential Expression in an Unsupervised Setting
dexus.parallel | A parallel version of DEXUS.
DEXUSResult-class | Class '"DEXUSResult"'
dispersions | Accessors for a "DEXUSResult".
dispersions-method | Class '"DEXUSResult"'
getSizeNB | Maximum-likelihood and maximum-a-posteriori estimators for the negative binomial distribution.
INI | I/NI filtering of a DEXUS result.
INI-method | Class '"DEXUSResult"'
INICalls | Accessors for a "DEXUSResult".
INICalls-method | Class '"DEXUSResult"'
INIThreshold | Accessors for a "DEXUSResult".
INIThreshold-method | Class '"DEXUSResult"'
INIThreshold-set | Set the I/NI threshold.
INIThreshold<- | Set the I/NI threshold.
INIThreshold<--method | Class '"DEXUSResult"'
INIValues | Accessors for a "DEXUSResult".
INIValues-method | Class '"DEXUSResult"'
inputData | Accessors for a "DEXUSResult".
inputData-method | Class '"DEXUSResult"'
logFC | Accessors for a "DEXUSResult".
logFC-method | Class '"DEXUSResult"'
means | Accessors for a "DEXUSResult".
means-method | Class '"DEXUSResult"'
normalizeData | Normalization of RNA-Seq count data.
normalizedData | Accessors for a "DEXUSResult".
normalizedData-method | Class '"DEXUSResult"'
params | Accessors for a "DEXUSResult".
params-method | Class '"DEXUSResult"'
plot | Visualization of a result of the DEXUS algorithm.
plot-method | Class '"DEXUSResult"'
posteriorProbs | Accessors for a "DEXUSResult".
posteriorProbs-method | Class '"DEXUSResult"'
pvals | Accessors for a "DEXUSResult".
pvals-method | Class '"DEXUSResult"'
responsibilities | Accessors for a "DEXUSResult".
responsibilities-method | Class '"DEXUSResult"'
sampleNames | Accessors for a "DEXUSResult".
sampleNames-method | Class '"DEXUSResult"'
show-method | Class '"DEXUSResult"'
sizeFactors | Accessors for a "DEXUSResult".
sizeFactors-method | Class '"DEXUSResult"'
sizeParameters | Accessors for a "DEXUSResult".
sizeParameters-method | Class '"DEXUSResult"'
sort | Sorting a DEXUS result.
sort-method | Class '"DEXUSResult"'
transcriptNames | Accessors for a "DEXUSResult".
transcriptNames-method | Class '"DEXUSResult"'
[-method | Class '"DEXUSResult"'
`[` | Subsetting a "DEXUSResult".
`[`-method | Subsetting a "DEXUSResult".