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>
citation("SCFA")):
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")| SCFA package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, Software, Survival |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | LGPL |
| Depends | R (>= 4.0) |
| Imports | matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix, cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival |
| System Requirements | |
| URL | https://github.com/duct317/SCFA |
| Bug Reports | https://github.com/duct317/SCFA/issues |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SCFA/ |
| Package Short Url | https://bioconductor.org/packages/SCFA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |