SIBER: Systematic Identification of Bimodally Expressed Genes Using RNAseq Data
Version 1.0.0

SIBER(Systematic Identification of Bimodally Expressed genes using RNAseq data) effectively identifies bimodally expressed genes from RNAseq data based on Bimodality Index. SIBER models the RNAseq data in the finite mixture modeling framework and incorporates mechanisms for dealing with RNAseq normalization. Three types of mixture models are implemented, namely, the mixture of log normal, negative binomial, or generalized poisson distribution.

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AuthorPan Tong, Kevin R Coombes
Date of publication2015-05-26 18:32:12
MaintainerPan Tong <nickytong@gmail.com>
LicenseApache License (== 2.0)
Version1.0.0
URL http://oompa.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SIBER", repos="http://R-Forge.R-project.org")

Man pages

fitGP: Fit Generalized Poisson Mixture Model
fitLN: Fit Log Normal Mixture Model
fitNB: Fit Negative Binomial Mixture Model
fitNL: Fit Negative Binomial Mixture Model
SIBER: Fit Mixture Model on The RNAseq Data and Calculates...
simDat: Simulated Data From 2-component Mixture Models

Functions

SIBER Man page Source code
dataList Man page
extractMclustPar Source code
fitGP Man page Source code
fitLN Man page Source code
fitNB Man page Source code
fitNL Man page Source code
getBIC Source code
logLik0inflatedLN Source code
logLikGenPoi0inflByOverdisp Source code
logLikGenPoiMixByOverdisp Source code
logLikGenPoiOneCompByOverdisp Source code
logLikLN Source code
logLikNegBin0inflByOverdisp Source code
logLikNegBinMixByOverdisp Source code
logLikNegBinOneCompByOverdisp Source code
muPhiToVar Source code Source code
muVarToPhi Source code
parList Man page
parToBI Source code
simDat Man page
transformPhiToSigmaInMixFit Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/siberRaw2.R
build
build/vignette.rds
data
data/simDat.rda
inst
inst/doc
inst/doc/SIBER.R
inst/doc/SIBER.Rnw
inst/doc/SIBER.pdf
man
man/SIBER.Rd
man/fitGP.Rd
man/fitLN.Rd
man/fitNB.Rd
man/fitNL.Rd
man/simDat.Rd
vignettes
vignettes/SIBER.Rnw
vignettes/siber.bib
SIBER documentation built on May 21, 2017, 1:14 a.m.