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. |