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

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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.