beta.mom                Fit the beta distribution by method of moments
crit_fun                Calculate the soft threshold for a target FDR
DenNHist                Density plot to compare the empirical q's and
                        the simulated q's from the fitted beta
                        distribution.
EBMultiTest             Using EM algorithm to calculate the posterior
                        probabilities of interested patterns in a
                        multiple condition study
EBSeq_NingLeng-package
                        EBSeq: RNA-Seq Differential Expression Analysis
                        on both gene and isoform level
EBSeqTest               EBSeq core
EBTest                  Using EM algorithm to calculate the posterior
                        probabilities of being DE
f0                      The Prior Predictive Distribution of being EE
f1                      The Prior Predictive Distribution of being DE
GeneMat                 The simulated data for two condition gene DE
                        analysis
GetDEResults            Obtain Differential Expression Analysis Results
                        in a Two-condition Test
GetMultiFC              Calculate the Fold Changes for Multiple
                        Conditions
GetMultiPP              Posterior Probability of Each Transcript
GetNg                   Ng Vector
GetNormalizedMat        Calculate normalized expression matrix
GetPatterns             Generate all possible patterns in a multiple
                        condition study
GetPPMat                Posterior Probability of Transcripts
GetSelectedPatterns     Get selected patterns in a multiple condition
                        study
IsoList                 The simulated data for two condition isoform DE
                        analysis
IsoMultiList            The simulated data for multiple condition
                        isoform DE analysis
Likefun                 Likelihood Function of the NB-Beta Model
LikefunMulti            Likelihood Function of the NB-Beta Model In
                        Multiple Condition Test
LogN                    The function to run EM (one round) algorithm
                        for the NB-beta model.
LogNMulti               EM algorithm for the NB-beta model in the
                        multiple condition test
MedianNorm              Median Normalization
MultiGeneMat            The simulated data for multiple condition gene
                        DE analysis
PlotPattern             Visualize the patterns
PlotPostVsRawFC         Plot Posterior FC vs FC
PolyFitPlot             Fit the mean-var relationship using polynomial
                        regression
PostFC                  Calculate the posterior fold change for each
                        transcript across conditions
QQP                     The Quantile-Quantile Plot to compare the
                        empirical q's and simulated q's from fitted
                        beta distribution
QuantileNorm            Quantile Normalization
RankNorm                Rank Normalization
