Package: TOP 1.7.0
Harry Robertson
TOP: TOP Constructs Transferable Model Across Gene Expression Platforms
TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.
Authors:
TOP_1.7.0.tar.gz
TOP_1.7.0.zip(r-4.5)TOP_1.7.0.zip(r-4.4)TOP_1.7.0.zip(r-4.3)
TOP_1.7.0.tgz(r-4.5-any)TOP_1.7.0.tgz(r-4.4-any)TOP_1.7.0.tgz(r-4.3-any)
TOP_1.7.0.tar.gz(r-4.5-noble)TOP_1.7.0.tar.gz(r-4.4-noble)
TOP_1.7.0.tgz(r-4.4-emscripten)TOP_1.7.0.tgz(r-4.3-emscripten)
TOP.pdf |TOP.html✨
TOP/json (API)
| # Install 'TOP' in R: |
| install.packages('TOP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/harry25r/top/issues
- TOP_data_binary - A simulated binary data
On BioConductor:TOP-1.7.0(bioc 3.21)TOP-1.6.0(bioc 3.20)
softwaresurvivalgeneexpression
Last updated 4 months agofrom:ade71fec18. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win | NOTE | Feb 28 2025 |
| R-4.5-mac | NOTE | Feb 28 2025 |
| R-4.5-linux | NOTE | Feb 28 2025 |
| R-4.4-win | NOTE | Feb 28 2025 |
| R-4.4-mac | NOTE | Feb 28 2025 |
| R-4.3-win | NOTE | Feb 28 2025 |
| R-4.3-mac | NOTE | Feb 28 2025 |
Exports:coefNetworkPlotexpitfilterFeaturespairwise_col_diffperformance_TOPpredict_TOPROC_PlotsimplenetworkPlotSurv_TOP_CITOP_coefPlotTOP_lambdaPlotTOP_modelTOP_survivalTOP_survivalPrediction
Dependencies:abindannotateAnnotationDbiaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringsbitbit64blobbootbroombslibcachemcalibratecarcarDatacaretcheckmatecirclizeclassClassifyRcliclockclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdcanrDelayedArrayDerivdiagramdigestdirectPAdoBydoParalleldoRNGdplyre1071evaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggnewscaleggplot2ggpubrggraphggrepelggsciggsignifggthemesggupsetglmnetGlobalOptionsglobalsgluegowergraphlayoutsgridExtragtablehardhathighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatex2explatticelavalazyevallifecyclelimmalistenvlme4lubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqaModelMetricsmodelrMultiAssayExperimentmunsellnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgconfigplogrplotlyplyrpngpolyclippolynompROCprodlimprogressrpromisesproxypurrrquantregR6rangerrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrecipesreformulasreshape2rlangrmarkdownrngtoolsrpartRSQLiterstatixrstudioapiS4ArraysS4VectorssassscalesshapesnowSparseArraySparseMsparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttimechangetimeDatetinytextweenrtzdbUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| coefNetworkPlot | coefNetworkPlot |
| The expit function | expit |
| filterFeatures | filterFeatures |
| Compute pairwise difference between matrix columns | pairwise_col_diff |
| performance_TOP | performance_TOP |
| Prectict using the Trasferable Omics Prediction model. | predict_TOP |
| ROC_Plot | ROC_Plot |
| simplenetworkPlot | simplenetworkPlot |
| Create a function to calculate the concordance index. | Surv_TOP_CI |
| TOP_coefPlot | TOP_coefPlot |
| A simulated binary data | TOP_data_binary |
| TOP_lambdaPlot | TOP_lambdaPlot |
| TOP_model | TOP_model |
| TOP_survival | TOP_survival |
| TOP_survivalPrediction | TOP_survivalPrediction |