Negative Binomial Models for RNA-Sequencing Data

Documentation for package ‘NBPSeq’ version 0.3.1

NBPSeq-package	Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data
arab	Arabidopsis RNA-Seq Data Set
estimate.disp	Fit a parametric disperison model to thinned counts
estimate.dispersion	Estimate Negative Binomial Dispersion
estimate.norm.factors	Estiamte Normalization Factors
exact.nb.test	Exact Negative Binomial Test for Differential Gene Expression
irls.nb.1	Estimate the regression coefficients in an NB GLM model
nb.glm.test	Fit Negative Binomial Regression Model and Test for a Regression Coefficient
nbp.test	NBP Test for Differential Gene Expression from RNA-Seq Counts
NBPSeq	Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data
plot.nb.data	Boxplot and scatterplot matrix of relative frequencies (after normalization)
plot.nb.dispersion	Plot the estimated dispersion as a function of the preliminarily estimated mean relative frequencies
plot.nbp	Diagnostic Plots for an NBP Object
prepare.nb.data	Prepare the NB Data Structure for RNA-Seq Read Counts
prepare.nbp	Prepare the Data Structure for Exact NB test for Two-Group Comparison
print.nb.data	Print summary of the nb counts
print.nb.dispersion	Print the estimated dispersion model
print.nb.test	Print output from 'test.coefficient'
print.nbp	Print summary of an NBP Object
test.coefficient	Large-sample Test for a Regression Coefficient in an Negative Binomial Regression Model