Test for differential expression for RNA-seq data

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Documentation for package ‘XBSeq’ version 1.20.0

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XBSeq-package Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
apaUsage Testing differential alternative polyadenylation (apa) usage by using roar
Background Example Datasets used in the manual pages as well as in vignette
conditions Accessor functions for the 'conditions' information in a XBSeqDataSet object.
conditions-method Accessor functions for the 'conditions' information in a XBSeqDataSet object.
conditions<--method Accessor functions for the 'conditions' information in a XBSeqDataSet object.
counts Accessor functions for the 'counts' information in a XBSeqDataSet object.
counts-method Accessor functions for the 'counts' information in a XBSeqDataSet object.
dispEst Function to access the dispersion estimation for each gene
dispEst-method Function to access the dispersion estimation for each gene
dispEst<- Function to access the dispersion estimation for each gene
dispEst<--method Function to access the dispersion estimation for each gene
dispTable Access the dispersion table information for a XBSeqDataSet object
dispTable-method Access the dispersion table information for a XBSeqDataSet object
estimateRealCount Preliminary step to estimate the true signal based on observed signal and background noise
estimateRealCount-method Preliminary step to estimate the true signal based on observed signal and background noise
estimateSCV Estimate squared coefficient of variation for each gene
estimateSCV-method Estimate squared coefficient of variation for each gene
ExampleData Example Datasets used in the manual pages as well as in vignette
fitInfo Accessor function for the fitInfo objects in a XBSeqDataSet
fitInfo-method Accessor function for the fitInfo objects in a XBSeqDataSet
genelength Example Datasets used in the manual pages as well as in vignette
getSignalVars Estimate variance of the signal based on variance summation law
MAplot Generate maplot after differential expression test
Observed Example Datasets used in the manual pages as well as in vignette
plotSCVEsts Plot estimated squared coefficient of variation
scvBiasCorrectionFits Estimate squared coefficient of variation for each gene
XBplot Examine the distribution of observed signal and background noise
XBSeq Express function to carry out XBSeq analysis
XBSeqDataSet Class '"XBSeqDataSet"'
XBSeqDataSet-class Class '"XBSeqDataSet"'
XBSeqTest XBSeq test for differential expression