# Test for differential expression for RNA-seq data

## Documentation for package ‘XBSeq’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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