Package: ABSSeq 1.61.0

Wentao Yang

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.

Authors:Wentao Yang

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ABSSeq.pdf |ABSSeq.html✨
ABSSeq/json (API)
NEWS

# Install 'ABSSeq' in R:
install.packages('ABSSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • simuN5 - Simulated study with random outliers

On BioConductor:ABSSeq-1.59.0(bioc 3.20)ABSSeq-1.58.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialexpression

3.78 score 1 packages 1 scripts 406 downloads 34 exports 4 dependencies

Last updated 23 days agofrom:15bbde7dce. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:ABSDataSetABSSeqABSSeqlmaFoldcomplexDesigncallDEscallParametercallParameterwithoutReplicatescountscounts<-estimateSizeFactorsForMatrixexcountsexcounts<-genAFoldgroupsgroups<-LevelstoNormFCLevelstoNormFC<-maxRatesmaxRates<-minimalDispersionminimalDispersion<-minRatesminRates<-normalFactorsnormMethodnormMethod<-pairedpaired<-plotDifftoBaseqtotalNormalizedReplaceOutliersByMADresultssFactorssFactors<-

Dependencies:latticelimmalocfitstatmod

ABSSeq

Rendered fromABSSeq.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2017-08-30
Started: 2014-03-27

Readme and manuals

Help Manual

Help pageTopics
ABSDataSet object and constructorsABSDataSet ABSDataSet-class SumInfo-class [[<-,SumInfo,character,missing-method
Differential expression analysis based on the total counts difference.ABSSeq
Differential expression analysis for complex desgin.ABSSeqlm
Calculate parameters for differential expression test base on absolute counts differencesaFoldcomplexDesign
Testing the differential expression by counts differencecallDEs
Calculate parameters for differential expression test base on absolute counts differencescallParameter
Calculate parameters for differential expression test base on absolute counts differences without replicatescallParameterwithoutReplicates
Accessors for the 'counts' slot of a ABSDataSet object.counts counts,ABSDataSet-method counts<- counts<-,ABSDataSet,matrix-method
Low-level function to estimate size factors with robust regression.estimateSizeFactorsForMatrix
Accessors for the 'excounts' slot of a ABSDataSet object.excounts excounts,ABSDataSet-method excounts<- excounts<-,ABSDataSet,matrix-method
Calculate parameters for differential expression test base on absolute counts differencesgenAFold
Accessors for the 'groups' slot of a ABSDataSet object.groups groups,ABSDataSet-method groups<- groups<-,ABSDataSet,factor-method
Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object.LevelstoNormFC LevelstoNormFC,ABSDataSet-method LevelstoNormFC<- LevelstoNormFC<-,ABSDataSet,numeric-method
Accessors for the 'maxRates' slot of a ABSDataSet object.maxRates maxRates,ABSDataSet-method maxRates<- maxRates<-,ABSDataSet,numeric-method
Accessors for the 'minDispersion' slot of a ABSDataSet object.minimalDispersion minimalDispersion,ABSDataSet-method minimalDispersion<- minimalDispersion<-,ABSDataSet,numeric-method
Accessors for the 'minRates' slot of a ABSDataSet object.minRates minRates,ABSDataSet-method minRates<- minRates<-,ABSDataSet,numeric-method
Estimating size factors from the reads count tablenormalFactors
Accessors for the 'normMethod' slot of a ABSDataSet object.normMethod normMethod,ABSDataSet-method normMethod<- normMethod<-,ABSDataSet,character-method
Accessors for the 'paired' slot of a ABSDataSet object.paired paired,ABSDataSet-method paired<- paired<-,ABSDataSet,logical-method
Plot absolute log2 fold-change against base mean of expressionplotDifftoBase
Estimating size factors from the reads count table via rankingqtotalNormalized
Replacing outliers by moderated MADReplaceOutliersByMAD
Accessor functions for the result from a ABSDataSetresults results,ABSDataSet-method
Accessors for the 'sizeFactor' slot of a ABSDataSet object.sFactors sFactors,ABSDataSet-method sFactors<- sFactors<-,ABSDataSet,numeric-method
Simulated study with random outlierssimuN5