NBPSeq (version 0.3.1)

Negative Binomial Models for RNA-Sequencing Data

Description

Negative Binomial (NB) models for two-group comparisons and regression inferences from RNA-Sequencing Data.

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Version

Install

install.packages('NBPSeq')

Monthly Downloads

369

Version

0.3.1

License

GPL-2

Maintainer

Yanming Di

Last Published

June 9th, 2022

Functions in NBPSeq (0.3.1)

estimate.disp

Fit a parametric disperison model to thinned counts

irls.nb.1

Estimate the regression coefficients in an NB GLM model

nbp.test

NBP Test for Differential Gene Expression from RNA-Seq Counts

estimate.norm.factors

Estiamte Normalization Factors

NBPSeq-package

Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data

nb.glm.test

Fit Negative Binomial Regression Model and Test for a Regression Coefficient

estimate.dispersion

Estimate Negative Binomial Dispersion

arab

Arabidopsis RNA-Seq Data Set

exact.nb.test

Exact Negative Binomial Test for Differential Gene Expression

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

test.coefficient

Large-sample Test for a Regression Coefficient in an Negative Binomial Regression Model

print.nb.dispersion

Print the estimated dispersion model

print.nb.data

Print summary of the nb counts

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

plot.nbp

Diagnostic Plots for an NBP Object

print.nbp

Print summary of an NBP Object

print.nb.test

Print output from test.coefficient