Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

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Documentation for package ‘sSeq’ version 1.45.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

sSeq-package	Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
countsTable	An Example Simulation Data
drawMA_vol	Draw MA Plot and Volcano Plot
ecdfAUC	Draw Empirical Cumulative Density Function (ECDF) plot
equalSpace	Calculate Grouped Shrinkage Estimates
exactNBtest1	Perform only one exact test under the Negative Binomial modeling.
getAdjustDisp	Calculate Shrinkage (SH) Estimates for Dispersion
getNormFactor	Estimate size factors
getQ	Estimate the shrinkage target based on the quantiles of initial targets
getT	Estimate the shrinkage target based on the initial estimates
getTgroup	This is an internal function used to calculate the shrinkage estimation when multiple shrinkage targets are considered.
Hammer2months	An example of real experiment.
nbinomTestForMatricesSH	Exact test under Negative Binomial Test with Shrinkage Estimates on Dispersions
nbTestSH	Differential Analysis based on RNA-seq experiments using Negative Binomial (NB) Model with Shrinkage Approach of Dispersion Estimation.
plotDispersion	Drawing Dispersion-Mean plot.
rnbinomMV	Randomly Generate Negative Binomial Variable with parameters mean and variance.
rowVars	Calculating the sample variance within each row of A matrix
sim	Generating Simulated Data
sSeq	Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Sultan	An example of real experiment.
Tuch	An example of real experiment.