EBSeqHMM: Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Version 1.10.0

The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). The EBSeqHMM package provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.

AuthorNing Leng, Christina Kendziorski
Bioconductor views Bayesian DifferentialExpression GeneExpression HiddenMarkovModel MultipleComparison RNASeq Sequencing StatisticalMethod TimeCourse
Date of publicationNone
MaintainerNing Leng <lengning1@gmail.com>
LicenseArtistic-2.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EBSeqHMM")

Getting started

Package overview

Popular man pages

beta.mom: Method of moments estimation ( beta distribution )
EBHMMNBfunForMulti: Baum-Welch algorithm for multiple hidden markov chains
EBSeqHMM-package: EBSeqHMM: A Bayesian approach for identifying gene-expression...
EBSeqHMMTest: Identify DE genes and classify them into their most likely...
EBTest_ext: Extented EBTest function
f0: Calculate the prior predictive distribution of the...
PlotExp: Plot expression of a single gene
See all...

All man pages Function index File listing

Man pages

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-package: EBSeqHMM: A Bayesian approach for identifying gene-expression...
EBSeqHMMTest: Identify DE genes and classify them into their most likely...
EBTest_ext: Extented EBTest function
f0: Calculate the prior predictive distribution of the...
GeneExampleData: Simulated gene level data set with 5 ordered conditions
GetAllPaths: Obtain all possible gene paths for an RNA-seq experiments...
GetConfidentCalls: Obtain confident gene calls for classifying genes into...
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

Functions

EBHMMNBMultiEM_2chain Man page Source code
EBHMMNBfun Man page Source code
EBHMMNBfunForMulti Man page Source code
EBSeqHMM Man page
EBSeqHMM-package Man page
EBSeqHMMTest Man page Source code
EBTest_ext Man page Source code
GeneExampleData Man page
GetAllPaths Man page Source code
GetConfidentCalls Man page Source code
GetDECalls Man page Source code
IsoExampleList Man page
LikefunNBHMM Man page Source code
PlotExp Man page Source code
beta.mom Man page Source code
f0 Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/EBHMMNBMultiEM_2chain.R
R/EBHMMNBfun.R
R/EBHMMNBfunForMulti.R
R/EBSeqHMMTest.R
R/EBTest_ext.R
R/GetAllPaths.R
R/GetConfidentCalls.R
R/GetDECalls.R
R/LikefunNBHMM.R
R/PlotExp.R
R/beta.mom.R
R/f0.R
build
build/vignette.rds
data
data/GeneExampleData.rda
data/IsoExampleList.rda
demo
demo/00Index
demo/EBSeqHMM.R
inst
inst/doc
inst/doc/EBSeqHMM_vignette.R
inst/doc/EBSeqHMM_vignette.Rnw
inst/doc/EBSeqHMM_vignette.pdf
man
man/EBHMMNBMultiEM_2chain.Rd
man/EBHMMNBfun.Rd
man/EBHMMNBfunForMulti.Rd
man/EBSeqHMM-package.Rd
man/EBSeqHMMTest.Rd
man/EBTest_ext.Rd
man/GeneExampleData.Rd
man/GetAllPaths.Rd
man/GetConfidentCalls.Rd
man/GetDECalls.Rd
man/IsoExampleList.Rd
man/LikefunNBHMM.Rd
man/PlotExp.Rd
man/beta.mom.Rd
man/f0.Rd
vignettes
vignettes/Diag_EBSeqHMM.pdf
vignettes/EBSeqHMM_vignette.Rnw
vignettes/lengetal.bib
vignettes/natbib.bst
vignettes/natbib.sty
EBSeqHMM documentation built on May 20, 2017, 10:06 p.m.

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