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

Share:

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.

Author
Ning Leng, Christina Kendziorski
Date of publication
None
Maintainer
Ning Leng <lengning1@gmail.com>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

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

Files in this package

EBSeqHMM/DESCRIPTION
EBSeqHMM/NAMESPACE
EBSeqHMM/NEWS
EBSeqHMM/R
EBSeqHMM/R/EBHMMNBMultiEM_2chain.R
EBSeqHMM/R/EBHMMNBfun.R
EBSeqHMM/R/EBHMMNBfunForMulti.R
EBSeqHMM/R/EBSeqHMMTest.R
EBSeqHMM/R/EBTest_ext.R
EBSeqHMM/R/GetAllPaths.R
EBSeqHMM/R/GetConfidentCalls.R
EBSeqHMM/R/GetDECalls.R
EBSeqHMM/R/LikefunNBHMM.R
EBSeqHMM/R/PlotExp.R
EBSeqHMM/R/beta.mom.R
EBSeqHMM/R/f0.R
EBSeqHMM/build
EBSeqHMM/build/vignette.rds
EBSeqHMM/data
EBSeqHMM/data/GeneExampleData.rda
EBSeqHMM/data/IsoExampleList.rda
EBSeqHMM/demo
EBSeqHMM/demo/00Index
EBSeqHMM/demo/EBSeqHMM.R
EBSeqHMM/inst
EBSeqHMM/inst/doc
EBSeqHMM/inst/doc/EBSeqHMM_vignette.R
EBSeqHMM/inst/doc/EBSeqHMM_vignette.Rnw
EBSeqHMM/inst/doc/EBSeqHMM_vignette.pdf
EBSeqHMM/man
EBSeqHMM/man/EBHMMNBMultiEM_2chain.Rd
EBSeqHMM/man/EBHMMNBfun.Rd
EBSeqHMM/man/EBHMMNBfunForMulti.Rd
EBSeqHMM/man/EBSeqHMM-package.Rd
EBSeqHMM/man/EBSeqHMMTest.Rd
EBSeqHMM/man/EBTest_ext.Rd
EBSeqHMM/man/GeneExampleData.Rd
EBSeqHMM/man/GetAllPaths.Rd
EBSeqHMM/man/GetConfidentCalls.Rd
EBSeqHMM/man/GetDECalls.Rd
EBSeqHMM/man/IsoExampleList.Rd
EBSeqHMM/man/LikefunNBHMM.Rd
EBSeqHMM/man/PlotExp.Rd
EBSeqHMM/man/beta.mom.Rd
EBSeqHMM/man/f0.Rd
EBSeqHMM/vignettes
EBSeqHMM/vignettes/Diag_EBSeqHMM.pdf
EBSeqHMM/vignettes/EBSeqHMM_vignette.Rnw
EBSeqHMM/vignettes/lengetal.bib
EBSeqHMM/vignettes/natbib.bst
EBSeqHMM/vignettes/natbib.sty