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


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Documentation for package ‘dexus’ version 1.4.0

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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".