# Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

## Documentation for package ‘EBSeqHMM’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

EBSeqHMM-package | EBSeqHMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
beta.mom | Method of moments estimation ( beta distribution )
EBHMMNBfun | Baum-Welch algorithm for a single hidden markov chain
EBHMMNBfunForMulti | Baum-Welch algorithm for multiple hidden markov chains
EBHMMNBMultiEM_2chain | Run EBSeqHMM model with a fixed expected FC
EBSeqHMM | 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
f0 | Calculate the prior predictive distribution of the Beta-Negative Binomial model
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