Package: pipeComp 1.23.4
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:
pipeComp_1.23.4.tar.gz
pipeComp_1.23.4.zip(r-4.7)pipeComp_1.23.4.zip(r-4.6)pipeComp_1.23.4.zip(r-4.5)
pipeComp_1.23.4.tgz(r-4.6-any)pipeComp_1.23.4.tgz(r-4.5-any)
pipeComp_1.23.4.tar.gz(r-4.7-any)pipeComp_1.23.4.tar.gz(r-4.6-any)
pipeComp_1.23.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pipeComp/json (API)
NEWS
| # Install 'pipeComp' in R: |
| install.packages('pipeComp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/plger/pipecomp/issues
- clustMetricsCorr - Correlations across clustering evaluation metrics
- ctrlgenes - Lists of control genes
- exampleDEAresults - Example results from the DEA pipeline
- exampleResults - Example pipeline results
- stableG - Lists of stable genes
On BioConductor:pipeComp-1.23.2(bioc 3.24)pipeComp-1.22.1(bioc 3.23)
geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq
Last updated from:7d4963a63f. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 250 | ||
| linux-devel-x86_64 | ERROR | 535 | ||
| source / vignettes | ERROR | 379 | ||
| linux-release-x86_64 | ERROR | 474 | ||
| macos-release-arm64 | ERROR | 337 | ||
| macos-oldrel-arm64 | ERROR | 273 | ||
| windows-devel | ERROR | 436 | ||
| windows-release | ERROR | 413 | ||
| windows-oldrel | ERROR | 396 | ||
| wasm-release | OK | 221 |
Exports:addPipelineStepaggregatePipelineResultsargumentsbuildCombMatrixcheckPipelinePackagescolCenterScaledea_evalPlot_curvedea_pipelinedefaultArgumentsdefaultArguments<-defaultStepAggregationevalHeatmapevaluateClusteringevaluateDEAevaluateDimRedevaluateNormfarthestPointgetQualitativePalettematch_evaluate_multiplemergePipelineResultsmockPipelineparsePipNamesPipelineDefinitionplotElapsedreadPipelineResultsrunPipelinescrna_describeDatasetsscrna_evalPlot_filteringscrna_evalPlot_overallscrna_evalPlot_silhscrna_pipelinestepFnstepFn<-
Dependencies:abindaricodeaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphintrinsicDimensionIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeminiUInlmeopensslotelparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6raggrandomcoloRRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscattermorescransctransformscuttleSeqinfoSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexutf8uwotV8vctrsviporviridisviridisLitewithrxfunxtableXVectoryaImputeyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| pipeComp - a framework for pipeline benchmarking | pipeComp-package pipeComp |
| addPipelineStep | addPipelineStep |
| aggregatePipelineResults | aggregatePipelineResults |
| buildCombMatrix | buildCombMatrix |
| checkPipelinePackages | checkPipelinePackages |
| Correlations across clustering evaluation metrics | clustMetricsCorr |
| colCenterScale | colCenterScale |
| Lists of control genes | ctrlgenes |
| dea_evalPlot_curve | dea_evalPlot_curve |
| dea_pipeline | dea_pipeline |
| defaultStepAggregation | defaultStepAggregation |
| evalHeatmap | evalHeatmap |
| evaluateClustering | evaluateClustering |
| evaluateDEA | evaluateDEA |
| evaluateDimRed | evaluateDimRed |
| evaluateNorm | evaluateNorm |
| Example results from the DEA pipeline | exampleDEAresults |
| Example pipeline results | exampleResults |
| farthestPoint | farthestPoint |
| getDimensionality | getDimensionality |
| getQualitativePalette | getQualitativePalette |
| match_evaluate_multiple | match_evaluate_multiple |
| mergePipelineResults | mergePipelineResults |
| mockPipeline | mockPipeline |
| parsePipNames | parsePipNames |
| PipelineDefinition | PipelineDefinition PipelineDefinition-class |
| Methods for 'PipelineDefinition' class | $,PipelineDefinition-method arguments arguments,PipelineDefinition-method as.list,PipelineDefinition-method defaultArguments defaultArguments,PipelineDefinition-method defaultArguments<- defaultArguments<-,PipelineDefinition-method length,PipelineDefinition-method names,PipelineDefinition-method names<-,PipelineDefinition-method PipelineDefinition-method PipelineDefinition-methods show,PipelineDefinition-method stepFn stepFn,PipelineDefinition-method stepFn<- stepFn<-,PipelineDefinition-method [,PipelineDefinition,ANY,ANY,ANY-method |
| plotElapsed | plotElapsed |
| readPipelineResults | readPipelineResults |
| runPipeline | runPipeline |
| scrna_describeDatasets | scrna_describeDatasets |
| scrna_evalPlot_filtering | scrna_evalPlot_filtering |
| scrna_evalPlot_overall | scrna_evalPlot_overall |
| scrna_evalPlot_silh | scrna_evalPlot_silh |
| scrna_pipeline | scrna_pipeline |
| Lists of stable genes | stableG |
