Introduction | Getting Started: FABIA | The FABIA Model | Class Factorization | Biclustering and Matrix Factorization Methods | Analyzing the Results of Biclustering / Matrix Factorization | Data Generation Methods | Utilities | Demo Data Sets from fabiaData
Package: fabia 2.59.0
Andreas Mitterecker
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.
Authors:
fabia_2.59.0.tar.gz
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fabia_2.59.0.tgz(r-4.6-x86_64)fabia_2.59.0.tgz(r-4.6-arm64)fabia_2.59.0.tgz(r-4.5-x86_64)fabia_2.59.0.tgz(r-4.5-arm64)
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fabia_2.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fabia/json (API)
| # Install 'fabia' in R: |
| install.packages('fabia', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:fabia-2.59.0(bioc 3.24)fabia-2.58.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
statisticalmethodmicroarraydifferentialexpressionmultiplecomparisonclusteringvisualization
Last updated from:13fa2a6383. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
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| bioc-checks | ERROR | 151 | ||
| linux-devel-arm64 | WARNING | 143 | ||
| linux-devel-x86_64 | WARNING | 200 | ||
| source / vignettes | OK | 179 | ||
| linux-release-arm64 | WARNING | 164 | ||
| linux-release-x86_64 | WARNING | 198 | ||
| macos-release-arm64 | WARNING | 126 | ||
| macos-release-x86_64 | WARNING | 190 | ||
| macos-oldrel-arm64 | WARNING | 100 | ||
| macos-oldrel-x86_64 | WARNING | 285 | ||
| windows-devel | WARNING | 105 | ||
| windows-release | WARNING | 124 | ||
| windows-oldrel | WARNING | 112 | ||
| wasm-release | OK | 94 |
Exports:aviniavini<-centercenter<-estimateModeextractBicextractPlotfabifabiafabiaDemofabiapfabiasfabiaspfabiaVersioniniini<-lLl<-L<-laplalapla<-LZLZ<-MM<-makeFabiaDatamakeFabiaDataBlocksmakeFabiaDataBlocksPosmakeFabiaDataPosmatrixImagePlotmfscnn<-nmfdivnmfeunmfscp1p1<-p2p2<-parametersparameters<-plotplotBiclusterprojFuncprojFuncPosPsiPsi<-readSamplesSpfabiareadSpfabiaResultsamplesPerFeaturescaleDatascaleData<-showshowSelectedspfabiasummaryUU<-XX<-xavinixavini<-ZZ<-
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimation of the modes of the rows of a matrix | estimateMode |
| Extraction of Biclusters | extractBic |
| Plotting of Biclustering Results | extractPlot |
| Factor Analysis for Bicluster Acquisition: Laplace Prior (FABI) | fabi |
| Factor Analysis for Bicluster Acquisition: Laplace Prior (FABIA) | fabia |
| Demos for fabia | fabiaDemo |
| Factor Analysis for Bicluster Acquisition: Post-Projection (FABIAP) | fabiap |
| Factor Analysis for Bicluster Acquisition: Sparseness Projection (FABIAS) | fabias |
| Factor Analysis for Bicluster Acquisition: Sparseness Projection (FABIASP) | fabiasp |
| Display version info for package and for FABIA | fabiaVersion |
| Factorization instances | avini avini,Factorization-method avini<- avini<-,Factorization,numeric-method avini<-,Factorization,vector-method center center,Factorization-method center<- center<-,Factorization,numeric-method center<-,Factorization,vector-method Factorization Factorization,ANY-method Factorization,list-method,numeric-method,vector-method,matrix-method,ANY-method Factorization-class Factorization-method ini ini,Factorization-method ini<- ini<-,Factorization,matrix-method L l L,Factorization-method l,Factorization-method L<- l<- L<-,Factorization,matrix-method l<-,Factorization,numeric-method lapla lapla,Factorization-method lapla<- lapla<-,Factorization,matrix-method LZ LZ,Factorization-method LZ<- LZ<-,Factorization,matrix-method M M,Factorization-method M<- M<-,Factorization,matrix-method n n,Factorization-method n<- n<-,Factorization,numeric-method p1 p1,Factorization-method p1<- p1<-,Factorization,numeric-method p2 p2,Factorization-method p2<- p2<-,Factorization,numeric-method parameters parameters,Factorization-method parameters<- parameters<-,Factorization,list-method plot,Factorization,missing-method plot,Factorization-method Psi Psi,Factorization-method Psi<- Psi<-,Factorization,numeric-method Psi<-,Factorization,vector-method scaleData scaleData,Factorization-method scaleData<- scaleData<-,Factorization,numeric-method scaleData<-,Factorization,vector-method show,Factorization-method showSelected showSelected,Factorization,numeric-method showSelected,Factorization-method summary,Factorization-method U U,Factorization-method U<- U<-,Factorization,matrix-method X X,Factorization-method X<- X<-,Factorization,matrix-method xavini xavini,Factorization-method xavini<- xavini<-,Factorization,numeric-method xavini<-,Factorization,vector-method Z Z,Factorization-method Z<- Z<-,Factorization,matrix-method |
| Generation of Bicluster Data | makeFabiaData |
| Generation of Bicluster Data with Bicluster Blocks | makeFabiaDataBlocks |
| Generation of Bicluster Data with Bicluster Blocks | makeFabiaDataBlocksPos |
| Generation of Bicluster Data | makeFabiaDataPos |
| Plotting of a Matrix | matrixImagePlot |
| Sparse Matrix Factorization for Bicluster Analysis (MFSC) | mfsc |
| Non-negative Matrix Factorization: Kullback-Leibler Divergence | nmfdiv |
| Non-negative Matrix Factorization: Euclidean Distance | nmfeu |
| Non-negative Sparse Matrix Factorization | nmfsc |
| Plotting of a bicluster | plotBicluster |
| Projection of a Vector to a Sparse Vector | projFunc |
| Projection of a Vector to a Non-negative Sparse Vector | projFuncPos |
| Factor Analysis for Bicluster Acquisition: Read Sparse Matrix Samples | readSamplesSpfabia |
| Factor Analysis for Bicluster Acquisition: Read Results of SpFabia | readSpfabiaResult |
| Factor Analysis for Bicluster Acquisition: Supplies samples per feature | samplesPerFeature |
| Factor Analysis for Bicluster Acquisition: SPARSE FABIA | spfabia |
