fabia
This is the development version of fabia; for the stable release version, see fabia.
FABIA: Factor Analysis for Bicluster Acquisition
Bioconductor version: Development (3.24)
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("fabia")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DifferentialExpression, Microarray, MultipleComparison, Software, StatisticalMethod, Visualization |
| Version | 2.59.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 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 |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | hapFabia |
| Imports Me | miRSM, mosbi |
| Suggests Me | fabiaData, SUMO |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fabia_2.59.0.tar.gz |
| Windows Binary (x86_64) | fabia_2.59.0.zip |
| macOS Binary (big-sur-x86_64) | fabia_2.59.0.tgz |
| macOS Binary (sonoma-arm64) | fabia_2.59.0.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/ |
| Package Downloads Report | Download Stats |