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

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Documentation for package ‘EBSeqHMM’ version 1.35.0

• 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