ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.

AuthorWentao Yang
Date of publicationNone
MaintainerWentao Yang <wyang@zoologie.uni-kiel.de>
LicenseGPL (>= 3)
Version1.20.4

View on Bioconductor

Man pages

ABSDataSet: ABSDataSet object and constructors

ABSSeq: Differential expression analysis based on the total counts...

callDEs: Testing the differential expression by counts difference

callParameter: Calculate parameters for differential expression test base on...

callParameterwithoutReplicates: Calculate parameters for differential expression test base on...

counts: Accessors for the 'counts' slot of a ABSDataSet object.

estimateSizeFactorsForMatrix: Low-level function to estimate size factors with robust...

excounts: Accessors for the 'excounts' slot of a ABSDataSet object.

genAFold: Calculate parameters for differential expression test base on...

groups: Accessors for the 'groups' slot of a ABSDataSet object.

LevelstoNormFC: Accessors for the 'LevelstoNormFC' slot of a ABSDataSet...

maxRates: Accessors for the 'maxRates' slot of a ABSDataSet object.

minimalDispersion: Accessors for the 'minDispersion' slot of a ABSDataSet...

minRates: Accessors for the 'minRates' slot of a ABSDataSet object.

normalFactors: Estimating size factors from the reads count table

normMethod: Accessors for the 'normMethod' slot of a ABSDataSet object.

paired: Accessors for the 'paired' slot of a ABSDataSet object.

plotDifftoBase: Plot absolute log2 fold-change against base mean of...

ReplaceOutliersByMAD: Replacing outliers by moderated MAD

results: Accessor functions for the result from a ABSDataSet

sFactors: Accessors for the 'sizeFactor' slot of a ABSDataSet object.

simuN5: Simulated study with random outliers

Functions

ABSDataSet Man page
ABSDataSet-class Man page
ABSSeq Man page
callDEs Man page
callParameter Man page
callParameterwithoutReplicates Man page
counts Man page
counts<- Man page
counts<-,ABSDataSet,matrix-method Man page
counts,ABSDataSet-method Man page
estimateSizeFactorsForMatrix Man page
excounts Man page
excounts<- Man page
excounts<-,ABSDataSet,matrix-method Man page
excounts,ABSDataSet-method Man page
genAFold Man page
groups Man page
groups<- Man page
groups<-,ABSDataSet,factor-method Man page
groups,ABSDataSet-method Man page
LevelstoNormFC Man page
LevelstoNormFC<- Man page
LevelstoNormFC,ABSDataSet-method Man page
LevelstoNormFC<-,ABSDataSet,numeric-method Man page
maxRates Man page
maxRates<- Man page
maxRates,ABSDataSet-method Man page
maxRates<-,ABSDataSet,numeric-method Man page
minimalDispersion Man page
minimalDispersion<- Man page
minimalDispersion,ABSDataSet-method Man page
minimalDispersion<-,ABSDataSet,numeric-method Man page
minRates Man page
minRates<- Man page
minRates,ABSDataSet-method Man page
minRates<-,ABSDataSet,numeric-method Man page
normalFactors Man page
normMethod Man page
normMethod<- Man page
normMethod<-,ABSDataSet,character-method Man page
normMethod,ABSDataSet-method Man page
paired Man page
paired<- Man page
paired<-,ABSDataSet,logical-method Man page
paired,ABSDataSet-method Man page
plotDifftoBase Man page
ReplaceOutliersByMAD Man page
results Man page
results,ABSDataSet-method Man page
sFactors Man page
sFactors<- Man page
sFactors,ABSDataSet-method Man page
sFactors<-,ABSDataSet,numeric-method Man page
simuN5 Man page
[[<-,SumInfo,character,missing-method Man page
SumInfo-class Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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