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


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Documentation for package ‘EBSeqHMM’ version 1.20.0

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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