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.

Author
Wentao Yang
Date of publication
None
Maintainer
Wentao Yang <wyang@zoologie.uni-kiel.de>
License
GPL (>= 3)
Version
1.10.0

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.
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

Files in this package

ABSSeq/DESCRIPTION
ABSSeq/NAMESPACE
ABSSeq/R
ABSSeq/R/AllClasses.R
ABSSeq/R/AllGenerics.R
ABSSeq/R/Plotfuns.R
ABSSeq/R/functions.R
ABSSeq/R/methods.R
ABSSeq/build
ABSSeq/build/vignette.rds
ABSSeq/data
ABSSeq/data/simuN5.rda
ABSSeq/inst
ABSSeq/inst/CITATION
ABSSeq/inst/NEWS
ABSSeq/inst/doc
ABSSeq/inst/doc/ABSSeq.R
ABSSeq/inst/doc/ABSSeq.Rnw
ABSSeq/inst/doc/ABSSeq.pdf
ABSSeq/man
ABSSeq/man/ABSDataSet.Rd
ABSSeq/man/ABSSeq.Rd
ABSSeq/man/LevelstoNormFC.Rd
ABSSeq/man/ReplaceOutliersByMAD.Rd
ABSSeq/man/callDEs.Rd
ABSSeq/man/callParameter.Rd
ABSSeq/man/callParameterwithoutReplicates.Rd
ABSSeq/man/counts.Rd
ABSSeq/man/estimateSizeFactorsForMatrix.Rd
ABSSeq/man/excounts.Rd
ABSSeq/man/groups.Rd
ABSSeq/man/maxRates.Rd
ABSSeq/man/minRates.Rd
ABSSeq/man/minimalDispersion.Rd
ABSSeq/man/normMethod.Rd
ABSSeq/man/normalFactors.Rd
ABSSeq/man/plotDifftoBase.Rd
ABSSeq/man/results.Rd
ABSSeq/man/sFactors.Rd
ABSSeq/man/simuN5.Rd
ABSSeq/vignettes
ABSSeq/vignettes/ABSSeq.Rnw