EBHMMNBMultiEM_2chain   Run EBSeqHMM model with a fixed expected FC
EBHMMNBfun              Baum-Welch algorithm for a single hidden markov
                        chain
EBHMMNBfunForMulti      Baum-Welch algorithm for multiple hidden markov
                        chains
EBSeqHMM-package        EBSeqHMM: A Bayesian approach for identifying
                        gene-expression changes in ordered RNA-seq
                        experiments
EBSeqHMMTest            Identify DE genes and classify them into their
                        most likely path in an RNA-seq experiment with
                        ordered conditions
EBTest_ext              Extented EBTest function
GeneExampleData         Simulated gene level data set with 5 ordered
                        conditions
GetAllPaths             Obtain all possible gene paths for an RNA-seq
                        experiments with ordered conditions
GetConfidentCalls       Obtain confident gene calls for classifying
                        genes into expression paths
GetDECalls              Obtain DE gene/isoform list at a certain FDR
IsoExampleList          Simulated isoform level data set with 5 ordered
                        conditions
LikefunNBHMM            Likelihood function of the Beta-Negative
                        Binomial HMM Model
PlotExp                 Plot expression of a single gene
beta.mom                Method of moments estimation ( beta
                        distribution )
f0                      Calculate the prior predictive distribution of
                        the Beta-Negative Binomial model
