MIMOSA: Mixture Models for Single-Cell Assays

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Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

Author
Greg Finak <gfinak@fhcrc.org>
Date of publication
None
Maintainer
Greg Finak <gfinak@fhcrc.org>
License
Artistic-2.0
Version
1.12.0

View on Bioconductor

Man pages

asinh_trans
asinh_trans
BetaMixResult-class
The output of fitting Beta-Binomial EM implementation...
boxplotMIMOSAResultList
boxplotMIMOSAResultList
combine.MIMOSA
Combine MIMOSAResultList objects
ConstructMIMOSAExpressionSet
A wrapper for constructing an Expression Set for MIMOSA
countsTable
Extract the table of counts from a MIMOSA model
fdr
Compute the fdr (q-value) from posterior probabilities
fitMCMC
Fit the MIMOSA model via MCMC
ICS
Stimulated and unstimulated T-cell counts for an ICS assay
MDMix
EM fitting of the Multinomial Dirichlet MIMOSA model.
MIMOSA
Fit a MIMOSA Model
MIMOSA-accessors
Extract the posterior probabilities of response from a MIMOSA...
MIMOSAExpressionSet
Construct an ExpressionSet for MIMOSA
MIMOSA-package
MIMOSA: Mixture Models for Single Cell Assays
MIMOSAResult
Stores the result of a MIMOSA fitted model
MIMOSAResult-class
Stores the result of a MIMOSA fitted model
pData
pData extract the phenoData table from a MIMOSA result
print
Print a MIMOSAResultList
show
show
volcanoPlot
Volcano plot for a MIMOSA model

Files in this package

MIMOSA/.travis.yml
MIMOSA/DESCRIPTION
MIMOSA/MIMOSA-Ex.pdf
MIMOSA/NAMESPACE
MIMOSA/NEWS
MIMOSA/R
MIMOSA/R/AllClasses.R
MIMOSA/R/BetaMix.R
MIMOSA/R/CompleteDataLL.R
MIMOSA/R/MIMOSA.R
MIMOSA/R/MarginalGT.R
MIMOSA/R/MarginalNE.R
MIMOSA/R/MarginalNULL.R
MIMOSA/R/MonteCarlo.R
MIMOSA/R/MultinomialDirichlet.R
MIMOSA/R/betaintegral.R
MIMOSA/R/constrained.R
MIMOSA/R/contourPlot.R
MIMOSA/R/gibbsPsPu.R
MIMOSA/R/helperMethods.R
MIMOSA/R/initBetaMix.R
MIMOSA/R/likelihoodsurface.R
MIMOSA/R/posteriorSample.R
MIMOSA/README.html
MIMOSA/README.md
MIMOSA/build
MIMOSA/build/vignette.rds
MIMOSA/data
MIMOSA/data/ICS.rda
MIMOSA/incubator
MIMOSA/incubator/server.R
MIMOSA/incubator/ui.R
MIMOSA/inst
MIMOSA/inst/CITATION
MIMOSA/inst/NEWS
MIMOSA/inst/doc
MIMOSA/inst/doc/MIMOSA.R
MIMOSA/inst/doc/MIMOSA.Rnw
MIMOSA/inst/doc/MIMOSA.pdf
MIMOSA/man
MIMOSA/man/BetaMixResult-class.Rd
MIMOSA/man/ConstructMIMOSAExpressionSet.Rd
MIMOSA/man/ICS.Rd
MIMOSA/man/MDMix.Rd
MIMOSA/man/MIMOSA-accessors.Rd
MIMOSA/man/MIMOSA-package.Rd
MIMOSA/man/MIMOSA.Rd
MIMOSA/man/MIMOSAExpressionSet.Rd
MIMOSA/man/MIMOSAResult-class.Rd
MIMOSA/man/MIMOSAResult.Rd
MIMOSA/man/asinh_trans.Rd
MIMOSA/man/boxplotMIMOSAResultList.Rd
MIMOSA/man/combine.MIMOSA.Rd
MIMOSA/man/countsTable.Rd
MIMOSA/man/fdr.Rd
MIMOSA/man/fitMCMC.Rd
MIMOSA/man/pData.Rd
MIMOSA/man/print.Rd
MIMOSA/man/show.Rd
MIMOSA/man/volcanoPlot.Rd
MIMOSA/src
MIMOSA/src/BetaMix.cpp
MIMOSA/src/MCMC.cpp
MIMOSA/src/MIMOSA.h
MIMOSA/src/MIMOSA_init.c
MIMOSA/src/Makevars
MIMOSA/src/Makevars.win
MIMOSA/src/betaintegral.c
MIMOSA/src/betaintegralRcpp.cpp
MIMOSA/tests
MIMOSA/tests/test-all.R
MIMOSA/tests/testthat
MIMOSA/tests/testthat/helper-init.R
MIMOSA/tests/testthat/test-MIMOSA.R
MIMOSA/vignettes
MIMOSA/vignettes/MIMOSA-concordance.tex
MIMOSA/vignettes/MIMOSA.Rnw