asuri
This is the development version of asuri; to use it, please install the devel version of Bioconductor.
Analysis of SUrvival and RIsk prediction in patients based on gene signatures
Bioconductor version: Development (3.23)
The ASURI (Analysis of SUrvival and patients RIsk prediction based on gene signatures) package discovers marker genes that are related to risk prediction capabilities and to a clinical variable of interest. It uses two main steps, including subsampling glmnet and unicox. The package implements robust functions to discover survival markers related to a clinical phenotype and to predict a risk score, allowing to study the patient's risk based on the gene signatures. Several plots are provided to visualise the relevance of the genes, the risk score, and patient stratification, as well as a robust version of the Kaplan-Meier curves.
Author: Alberto Berral-Gonzalez [aut, cre, ctb]
, Santiago Bueno-Fortes [aut, ctb]
, Natalia Alonso-Moreda [aut, ctb]
, Jose Manuel Sanchez-Santos [aut, ctb]
, Manuel Martin-Merino Acera [aut, ctb]
, Javier De Las Rivas [aut, ctb]
Maintainer: Alberto Berral-Gonzalez <aberralgonzalez at gmail.com>
citation("asuri")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("asuri")
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("asuri")| Asuri | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, ExonArray, GeneExpression, GenePrediction, Microarray, MultipleComparison, Regression, Software, StatisticalMethod, Survival, WorkflowStep |
| Version | 0.99.18 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | LGPL-3 + file LICENSE |
| Depends | R (>= 4.5.0), stats, methods |
| Imports | SummarizedExperiment, spsUtil, lubridate, survival, glmnet, siggenes, survcomp, scales, ROCR, ggplot2, grDevices, graphics, utils, Rdpack |
| System Requirements | |
| URL | https://github.com/jdelasrivas-lab/asuri |
| Bug Reports | https://github.com/jdelasrivas-lab/asuri/issues |
See More
| Suggests | BiocStyle, knitr, formatR, rmarkdown, magick, devtools |
| 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 | asuri_0.99.18.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | asuri_0.99.18.tgz |
| macOS Binary (arm64) | asuri_0.99.18.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/asuri |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/asuri |
| Bioc Package Browser | https://code.bioconductor.org/browse/asuri/ |
| Package Short Url | https://bioconductor.org/packages/asuri/ |
| Package Downloads Report | Download Stats |