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RLassoCox

A reweighted Lasso-Cox by integrating gene interaction information


Bioconductor version: Release (3.18)

RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.

Author: Wei Liu [cre, aut]

Maintainer: Wei Liu <freelw at qq.com>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("RLassoCox")

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("RLassoCox")
RLassoCox PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GenePrediction, Network, Regression, Software, Survival
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Depends R (>= 4.1), glmnet
Imports Matrix, igraph, survival, stats
System Requirements
URL
Bug Reports https://github.com/weiliu123/RLassoCox/issues
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Package Archives

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

Source Package RLassoCox_1.10.0.tar.gz
Windows Binary RLassoCox_1.10.0.zip
macOS Binary (x86_64) RLassoCox_1.10.0.tgz
macOS Binary (arm64) RLassoCox_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RLassoCox
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RLassoCox
Bioc Package Browser https://code.bioconductor.org/browse/RLassoCox/
Package Short Url https://bioconductor.org/packages/RLassoCox/
Package Downloads Report Download Stats