SCFA

DOI: 10.18129/B9.bioc.SCFA    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SCFA.

SCFA: Subtyping via Consensus Factor Analysis

Bioconductor version: 3.15

Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients.

Author: Duc Tran [aut, cre], Hung Nguyen [aut], Tin Nguyen [fnd]

Maintainer: Duc Tran <duct at nevada.unr.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("SCFA")

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("SCFA")

 

HTML	R Script	SCFA package manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, Software, Survival
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	LGPL
Depends	R (>= 4.0)
Imports	matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix, cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/duct317/SCFA
BugReports	https://github.com/duct317/SCFA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SCFA_1.6.0.tar.gz
Windows Binary	SCFA_1.6.0.zip (64-bit only)
macOS Binary (x86_64)	SCFA_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCFA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SCFA
Package Short Url	https://bioconductor.org/packages/SCFA/
Package Downloads Report	Download Stats