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fabia

This is the development version of fabia; for the stable release version, see fabia.

FABIA: Factor Analysis for Bicluster Acquisition


Bioconductor version: Development (3.19)

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.

Author: Sepp Hochreiter <hochreit at bioinf.jku.at>

Maintainer: Andreas Mitterecker <mitterecker at bioinf.jku.at>

Citation (from within R, enter citation("fabia")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("fabia")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("fabia")
FABIA: Manual for the R package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DifferentialExpression, Microarray, MultipleComparison, Software, StatisticalMethod, Visualization
Version 2.49.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License LGPL (>= 2.1)
Depends R (>= 3.6.0), Biobase
Imports methods, graphics, grDevices, stats, utils
System Requirements
URL http://www.bioinf.jku.at/software/fabia/fabia.html
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Linking To
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Depends On Me hapFabia
Imports Me miRSM, mosbi
Suggests Me fabiaData
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package fabia_2.49.0.tar.gz
Windows Binary fabia_2.49.0.zip
macOS Binary (x86_64) fabia_2.49.0.tgz
macOS Binary (arm64) fabia_2.49.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fabia
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fabia
Bioc Package Browser https://code.bioconductor.org/browse/fabia/
Package Short Url https://bioconductor.org/packages/fabia/
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