Package: pipeComp 1.15.0

Pierre-Luc Germain

pipeComp: pipeComp pipeline benchmarking framework

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

Authors:Pierre-Luc Germain [cre, aut], Anthony Sonrel [aut], Mark D. Robinson [aut, fnd]

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Bug tracker:https://github.com/plger/pipecomp/issues

On BioConductor:pipeComp-1.15.0(bioc 3.20)pipeComp-1.14.0(bioc 3.19)

bioconductor-package

33 exports 0.61 score 209 dependencies 1 mentions

Last updated 2 months agofrom:1356fefbef

Exports:addPipelineStepaggregatePipelineResultsargumentsbuildCombMatrixcheckPipelinePackagescolCenterScaledea_evalPlot_curvedea_pipelinedefaultArgumentsdefaultArguments<-defaultStepAggregationevalHeatmapevaluateClusteringevaluateDEAevaluateDimRedevaluateNormfarthestPointgetQualitativePalettematch_evaluate_multiplemergePipelineResultsmockPipelineparsePipNamesPipelineDefinitionplotElapsedreadPipelineResultsrunPipelinescrna_describeDatasetsscrna_evalPlot_filteringscrna_evalPlot_overallscrna_evalPlot_silhscrna_pipelinestepFnstepFn<-

Dependencies:abindaricodeaskpassbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphintrinsicDimensionIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6raggrandomcoloRRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotV8vctrsviporviridisviridisLitewithrxfunxtableXVectoryaImputeyamlzlibbioczoo