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.
|Date of publication||None|
|Maintainer||Wentao Yang <firstname.lastname@example.org>|
|License||GPL (>= 3)|
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.
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.
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