Package: Coxmos 1.2.0

Pedro Salguero
Coxmos: Cox MultiBlock Survival
This software package provides Cox survival analysis for high-dimensional and multiblock datasets. It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis, including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression, Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies, and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources for interpreting results. While references are available within the corresponding functions, key literature is mentioned below. Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>, Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>, Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>, Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009>, Philippe Bastien et al. (2014) <doi:10.1093/bioinformatics/btu660>, Kassu Mehari Beyene and Anouar El Ghouch (2020) <doi:10.1002/sim.8671>, Florian Rohart et al. (2017) <doi:10.1371/journal.pcbi.1005752>.
Authors:
Coxmos_1.2.0.tar.gz
Coxmos_1.2.0.zip(r-4.7)Coxmos_1.2.0.zip(r-4.6)Coxmos_1.2.0.zip(r-4.5)
Coxmos_1.2.0.tgz(r-4.6-x86_64)Coxmos_1.2.0.tgz(r-4.6-arm64)Coxmos_1.2.0.tgz(r-4.5-x86_64)Coxmos_1.2.0.tgz(r-4.5-arm64)
Coxmos_1.2.0.tar.gz(r-4.7-arm64)Coxmos_1.2.0.tar.gz(r-4.7-x86_64)Coxmos_1.2.0.tar.gz(r-4.6-arm64)Coxmos_1.2.0.tar.gz(r-4.6-x86_64)
Coxmos_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Coxmos/json (API)
| # Install 'Coxmos' in R: |
| install.packages('Coxmos', repos = c('https://biostatomics.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biostatomics/coxmos/issues
- X_multiomic - X_multiomic Data
- X_proteomic - X_proteomic Data
- Y_multiomic - Y_multiomic Data
- Y_proteomic - Y_proteomic Data
Last updated from:0c3bcb3778. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 346 | ||
| linux-devel-x86_64 | OK | 362 | ||
| source / vignettes | OK | 463 | ||
| linux-release-arm64 | OK | 342 | ||
| linux-release-x86_64 | OK | 366 | ||
| macos-release-arm64 | OK | 210 | ||
| macos-release-x86_64 | OK | 389 | ||
| macos-oldrel-arm64 | OK | 288 | ||
| macos-oldrel-x86_64 | OK | 466 | ||
| windows-devel | OK | 339 | ||
| windows-release | OK | 296 | ||
| windows-oldrel | OK | 254 | ||
| wasm-release | OK | 263 |
Exports:coxcox.predictioncoxENcoxmoscoxSWcv.coxENcv.coxmoscv.isb.splsdacoxcv.isb.splsdrcoxcv.isb.splsdrcox_penaltycv.isb.splsicoxcv.mb.coxmoscv.mb.splsdacoxcv.mb.splsdrcoxcv.sb.splsdacoxcv.sb.splsdrcoxcv.sb.splsdrcox_penaltycv.sb.splsicoxcv.splsdacoxcv.splsdrcoxcv.splsdrcox_penaltycv.splsicoxdeleteNearZeroCoefficientOfVariationdeleteNearZeroCoefficientOfVariation.mbdeleteZeroOrNearZeroVariabilitydeleteZeroOrNearZeroVariability.mbeval_Coxmos_model_per_variableeval_Coxmos_model_per_variable.listeval_Coxmos_modelsfactorToBinarygetAutoKMgetAutoKM.listgetCutoffAutoKMgetCutoffAutoKM.listgetDesign.MBgetEPVgetEPV.mbgetTestKMgetTestKM.listgetTrainTestisb.splsdacoxisb.splsdrcoxisb.splsdrcox_penaltyisb.splsicoxloadingplot.Coxmosmb.coxmosmb.splsdacoxmb.splsdrcoxplot_cox.eventplot_cox.event.listplot_divergent.biplotplot_evaluationplot_evaluation.listplot_eventsplot_forestplot_forest.listplot_multipleObservations.LPplot_multipleObservations.LP.listplot_observation.eventDensityplot_observation.eventHistogramplot_observation.pseudobetaplot_observation.pseudobeta.listplot_proportionalHazardplot_proportionalHazard.listplot_pseudobetaplot_pseudobeta.listplot_sPLS_Coxmosplot_time.listsave_ggplotsave_ggplot_lstsb.splsdacoxsb.splsdrcoxsb.splsdrcox_penaltysb.splsicoxsplsdacoxsplsdrcoxsplsdrcox_penaltysplsicoxtransformIllegalCharsw.starplot.Coxmos
Dependencies:abindbackportsbase64encBHBiocParallelbootbootstrapbroombslibcachemcarcarDatacaretclasscliclockcodetoolscolorspacecommonmarkcorpcorcorrplotcowplotcpp11crayoncurldata.tableDerivdiagramdigestdoBydplyre1071ellipseevaluateexactRankTestsfarverfastmapfontawesomeforeachforecastformatRFormulafracdifffsfurrrfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggpubrggrepelggsciggsignifggtextglmnetglobalsgluegowergridExtragridtextgtablehardhathighrhmshtmltoolshtmlwidgetsigraphipredisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelavalifecyclelistenvlitedownlme4lmtestlubridatemagrittrmarkdownMASSMatrixMatrixModelsmatrixStatsmaxstatmemoisemgcvmicrobenchmarkmimeminqamixOmicsModelMetricsmodelrmvtnormnlmenloptrnnetnumDerivparallellypatchworkpbkrtestpillarpkgconfigplyrpngpolynomprettyunitspROCprodlimprogressprogressrproxypurrrquantregR6rappdirsrARPACKrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrecipesreformulasreshape2rglrlangrmarkdownrmetarpartRSpectrarstatixS7sassscalesscattermoreshapesnowSparseMsparsevctrsSQUAREMstringistringrSuppDistssurvcompsurvivalsurvivalROCsurvminersvglitesystemfontstextshapingtibbletidyrtidyselecttimechangetimeDatetinytextzdburcautf8vctrsviridisLitewithrxfunxml2yamlzoo
Step-by-step guide to the High-Dimensional Coxmos pipeline
Rendered fromCoxmos-pipeline.Rmdusingknitr::rmarkdownon May 25 2026.Last update: 2025-06-02
Started: 2023-09-18
Step-by-step guide to the MultiBlock Coxmos pipeline
Rendered fromCoxmos-MO-pipeline.Rmdusingknitr::rmarkdownon May 25 2026.Last update: 2025-06-02
Started: 2023-09-18