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ABSSeq (version 1.8.0)

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

Description

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.

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Version

Version

1.8.0

License

GPL (>= 3)

Maintainer

Wentao Yang

Last Published

February 15th, 2017

Functions in ABSSeq (1.8.0)

minimalDispersion

Accessors for the 'minDispersion' slot of a ABSDataSet object.
callParameterwithoutReplicates

Calculate parameters for differential expression test base on absolute counts differences without replicates
groups

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

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

ABSDataSet object and constructors
normMethod

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

Estimating size factors from the reads count table
ABSSeq

Differential expression analysis based on the total counts difference.
LevelstoNormFC

Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object.
simuN5

Simulated study with random outliers
estimateSizeFactorsForMatrix

Low-level function to estimate size factors with robust regression.
maxRates

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

Calculate parameters for differential expression test base on absolute counts differences
excounts

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

Accessors for the 'sizeFactor' slot of a ABSDataSet object.
results

Accessor functions for the result from a ABSDataSet
callDEs

Testing the differential expression by counts difference
ReplaceOutliersByMAD

Replacing outliers by moderated MAD
counts

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

Plot absolute log2 fold-change against base mean of expression