Introduction | Package download and installation. Package dependencies. | Dataset description and download. | Platforms supported by the library and preprocessing. | Survival and risk assessment (case study on Breast Cancer). | Analysis of individual genes as survival markers: geneSurv() | Discovery of genes associated with phenotypic factors: genePheno() | Identification of gene survival markers & patient risk prediction: patientRisk() | Risk Prediction for an independent set of patients: predict_PatientRisk() | Survival estimation from the COX regression for a test patient: predict_SurvCurve() | Brief comparison of ASURI and other related R tools | Session Info | References
Package: asuri 1.1.0
Alberto Berral-Gonzalez
asuri: Analysis of SUrvival and RIsk prediction in patients based on gene signatures
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.
Authors:
asuri_1.1.0.tar.gz
asuri_1.1.0.zip(r-4.7)asuri_1.1.0.zip(r-4.6)asuri_1.1.0.zip(r-4.5)
asuri_1.1.0.tgz(r-4.6-any)asuri_1.1.0.tgz(r-4.5-any)
asuri_1.1.0.tar.gz(r-4.7-any)asuri_1.1.0.tar.gz(r-4.6-any)
asuri_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
asuri/json (API)
| # Install 'asuri' in R: |
| install.packages('asuri', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jdelasrivas-lab/asuri/issues
Datasets:
- ex_genePheno - Ex_genePheno
- ex_patientRisk - Ex_patientRisk
- ex_predictPatientRisk - Ex_predictPatientRisk
- ex_prefilterSAM - Ex_prefilterSAM
- seBRCA - Example SummarizedExperiment object
On BioConductor:asuri-1.1.0(bioc 3.24)asuri-1.0.0(bioc 3.23)
softwarestatisticalmethodworkflowstepgeneexpressionmicroarraydifferentialexpressiongenepredictionregressionsurvivalexonarraymultiplecomparison
Last updated from:dfe8e2e9b2. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 215 | ||
| linux-devel-x86_64 | NOTE | 507 | ||
| source / vignettes | OK | 419 | ||
| linux-release-x86_64 | NOTE | 496 | ||
| macos-release-arm64 | NOTE | 358 | ||
| macos-oldrel-arm64 | NOTE | 228 | ||
| windows-devel | NOTE | 507 | ||
| windows-release | NOTE | 475 | ||
| windows-oldrel | NOTE | 477 | ||
| wasm-release | OK | 183 |
Exports:genePhenogeneSurvpatientRiskplotBetasplotBoxplotplotKMplotLambdaplotLogRankplotProbClassplotSigmoidpredict_PatientRiskpredict_SurvCurveprefilterSAM
Dependencies:abindaskpassassertthatBiobaseBiocGenericsbitopsbootstrapcaToolsclassclicodetoolscpp11crayoncurldata.tableDelayedArraydiagramdigestfarverforeachfuturefuture.applygenericsGenomicRangesggplot2glmnetglobalsgluegplotsgtablegtoolshttripredIRangesisobanditeratorsjsonliteKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmimemulttestnnetnumDerivopensslparallellyprodlimprogressrR6rbibutilsRColorBrewerRcppRcppEigenRdpackrlangrmetaROCRrpartS4ArraysS4VectorsS7scalesscrimeSeqinfoshapesiggenesSparseArrayspsUtilSQUAREMstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsystimechangevctrsviridisLitewithrXVector
