Package: TOP 1.13.0

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:Harry Robertson [aut, cre], Nicholas Robertson [aut]

TOP_1.13.0.tar.gz
TOP_1.13.0.zip(r-4.7)TOP_1.13.0.zip(r-4.6)TOP_1.13.0.zip(r-4.5)
TOP_1.13.0.tgz(r-4.6-any)TOP_1.13.0.tgz(r-4.5-any)
TOP_1.13.0.tar.gz(r-4.7-any)TOP_1.13.0.tar.gz(r-4.6-any)
TOP_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Datasets:

On BioConductor:TOP-1.13.0(bioc 3.24)TOP-1.12.0(bioc 3.23)

softwaresurvivalgeneexpression

4.83 score 67 scripts 266 downloads 14 exports 213 dependencies

Last updated from:391b4a30ad. Checks:5 NOTE, 2 OK, 1 FAIL, 2 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE216
linux-devel-x86_64NOTE416
source / vignettesOK377
linux-release-x86_64NOTE401
macos-release-arm64FAIL103
macos-oldrel-arm64NOTE279
windows-develWARNING663
windows-releaseNOTE287
windows-oldrelWARNING636
wasm-releaseOK225

Exports:coefNetworkPlotexpitfilterFeaturespairwise_col_diffperformance_TOPpredict_TOPROC_PlotsimplenetworkPlotSurv_TOP_CITOP_coefPlotTOP_lambdaPlotTOP_modelTOP_survivalTOP_survivalPrediction

Dependencies:abindannotateAnnotationDbiaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringsbitbit64blobbootbroombslibcachemcalibratecarcarDatacaretcheckmatecirclizeclassClassifyRcliclockclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdcanrDelayedArrayDerivdiagramdigestdirectPAdoBydoParalleldoRNGdplyre1071evaluatefarverfastmapfontawesomeforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsfuturefuture.applygenefiltergenericsGenomicRangesggforceggnewscaleggplot2ggpubrggraphggrepelggsciggsignifggthemesggupsetglmnetGlobalOptionsglobalsgluegowergraphlayoutsgridExtragtablehardhathighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatex2explatticelavalazyevallifecyclelimmalistenvlme4lmtestlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqaModelMetricsmodelrMultiAssayExperimentnlmenloptrnnetnumDerivopensslotelparallellypbkrtestpillarpkgconfigplotlyplyrpngpolyclippolynompROCprodlimprogressrpromisesproxypurrrquantregR6rangerrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrecipesreformulasreshape2rlangrmarkdownrngtoolsrpartRSQLiterstatixrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraySparseMsparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttimechangetimeDatetinytextweenrtzdburcautf8vctrsviridisviridisLitewithrxfunXMLxtableXVectoryamlzoo

Tranferable Omics Pediction

Harry Robertson, Nicholas Robertson, Ellis Patrick

Rendered fromBuildingATOPModel.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2023-04-14
Started: 2023-01-24