fabia: FABIA: Factor Analysis for Bicluster Acquisition

Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.

AuthorSepp Hochreiter <hochreit@bioinf.jku.at>
Date of publicationNone
MaintainerSepp Hochreiter <hochreit@bioinf.jku.at>
LicenseLGPL (>= 2.1)
Version2.20.0
http://www.bioinf.jku.at/software/fabia/fabia.html

View on Bioconductor

Man pages

estimateMode: Estimation of the modes of the rows of a matrix

extractBic: Extraction of Biclusters

extractPlot: Plotting of Biclustering Results

fabi: Factor Analysis for Bicluster Acquisition: Laplace Prior...

fabia: Factor Analysis for Bicluster Acquisition: Laplace Prior...

fabiaDemo: Demos for fabia

fabiap: Factor Analysis for Bicluster Acquisition: Post-Projection...

fabias: Factor Analysis for Bicluster Acquisition: Sparseness...

fabiasp: Factor Analysis for Bicluster Acquisition: Sparseness...

fabiaVersion: Display version info for package and for FABIA

Factorization-class: Factorization instances

makeFabiaData: Generation of Bicluster Data

makeFabiaDataBlocks: Generation of Bicluster Data with Bicluster Blocks

makeFabiaDataBlocksPos: Generation of Bicluster Data with Bicluster Blocks

makeFabiaDataPos: Generation of Bicluster Data

matrixImagePlot: Plotting of a Matrix

mfsc: Sparse Matrix Factorization for Bicluster Analysis (MFSC)

nmfdiv: Non-negative Matrix Factorization: Kullback-Leibler...

nmfeu: Non-negative Matrix Factorization: Euclidean Distance

nmfsc: Non-negative Sparse Matrix Factorization

plotBicluster: Plotting of a bicluster

projFunc: Projection of a Vector to a Sparse Vector

projFuncPos: Projection of a Vector to a Non-negative Sparse Vector

readSamplesSpfabia: Factor Analysis for Bicluster Acquisition: Read Sparse Matrix...

readSpfabiaResult: Factor Analysis for Bicluster Acquisition: Read Results of...

samplesPerFeature: Factor Analysis for Bicluster Acquisition: Supplies samples...

spfabia: Factor Analysis for Bicluster Acquisition: SPARSE FABIA

Files in this package

fabia/DESCRIPTION
fabia/NAMESPACE
fabia/NEWS
fabia/R
fabia/R/AllClasses.R fabia/R/AllGenerics.R fabia/R/fabia.R fabia/R/methods-Factorization-class.R fabia/R/zzz.R
fabia/build
fabia/build/vignette.rds
fabia/cleanup
fabia/configure
fabia/configure.ac
fabia/configure.win
fabia/demo
fabia/demo/00Index
fabia/demo/demo01FabiaToydata.R
fabia/demo/demo02FabiaBreastcancer.R
fabia/demo/demo03FabiaMultipleTissues.R
fabia/demo/demo04FabiaLymphoma.R
fabia/demo/demo05FabiasToydata.R
fabia/demo/demo06FabiasBreastcancer.R
fabia/demo/demo07FabiasMultipleTissues.R
fabia/demo/demo08FabiasLymphoma.R
fabia/inst
fabia/inst/CITATION
fabia/inst/doc
fabia/inst/doc/fabia.R
fabia/inst/doc/fabia.Rnw
fabia/inst/doc/fabia.pdf
fabia/man
fabia/man/Factorization-class.Rd fabia/man/estimateMode.Rd fabia/man/extractBic.Rd fabia/man/extractPlot.Rd fabia/man/fabi.Rd fabia/man/fabia.Rd fabia/man/fabiaDemo.Rd fabia/man/fabiaVersion.Rd fabia/man/fabiap.Rd fabia/man/fabias.Rd fabia/man/fabiasp.Rd fabia/man/makeFabiaData.Rd fabia/man/makeFabiaDataBlocks.Rd fabia/man/makeFabiaDataBlocksPos.Rd fabia/man/makeFabiaDataPos.Rd fabia/man/matrixImagePlot.Rd fabia/man/mfsc.Rd fabia/man/nmfdiv.Rd fabia/man/nmfeu.Rd fabia/man/nmfsc.Rd fabia/man/plotBicluster.Rd fabia/man/projFunc.Rd fabia/man/projFuncPos.Rd fabia/man/readSamplesSpfabia.Rd fabia/man/readSpfabiaResult.Rd fabia/man/samplesPerFeature.Rd fabia/man/spfabia.Rd
fabia/src
fabia/src/Makefile.win
fabia/src/Makevars.in
fabia/src/fabiac.c
fabia/vignettes
fabia/vignettes/bioinf-article.txi
fabia/vignettes/bioinf-bar.png
fabia/vignettes/bioinf.cls
fabia/vignettes/fabia.Rnw
fabia/vignettes/fabia.bib
fabia/vignettes/fabia_defs.sty
fabia/vignettes/figures
fabia/vignettes/figures/fabia-lap1.eps
fabia/vignettes/figures/fabia-lap1.pdf
fabia/vignettes/figures/fabia-lap2.eps
fabia/vignettes/figures/fabia-lap2.pdf
fabia/vignettes/figures/vectors_1.eps
fabia/vignettes/figures/vectors_1.pdf
fabia/vignettes/natbib.bst
fabia/vignettes/natbib.sty

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