Package: pipeComp 1.22.1

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]

pipeComp_1.22.1.tar.gz
pipeComp_1.22.1.zip(r-4.7)pipeComp_1.22.1.zip(r-4.6)pipeComp_1.22.1.zip(r-4.5)
pipeComp_1.22.1.tgz(r-4.6-any)pipeComp_1.22.1.tgz(r-4.5-any)
pipeComp_1.22.1.tar.gz(r-4.7-any)pipeComp_1.22.1.tar.gz(r-4.6-any)
pipeComp_1.22.1.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-release.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

On BioConductor:pipeComp-1.23.2(bioc 3.24)pipeComp-1.22.0(bioc 3.23)

geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq

7.46 score 43 stars 45 scripts 346 downloads 1 mentions 33 exports 204 dependencies

Last updated from:6229cb18bc (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE261
linux-devel-x86_64WARNING540
source / vignettesOK383
linux-release-x86_64WARNING474
macos-release-arm64WARNING323
macos-oldrel-arm64WARNING283
windows-develWARNING418
windows-releaseWARNING445
windows-oldrelWARNING436
wasm-releaseOK207

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

The pipeComp framework

Rendered frompipeComp.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2020-09-04
Started: 2020-03-05

The DEA PipelineDefinition

Rendered frompipeComp_dea.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2020-04-29
Started: 2020-04-20

The scRNA PipelineDefinition

Rendered frompipeComp_scRNA.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2020-07-23
Started: 2020-03-05

Readme and manuals

Help Manual

Help pageTopics
pipeComp - a framework for pipeline benchmarkingpipeComp-package pipeComp
addPipelineStepaddPipelineStep
aggregatePipelineResultsaggregatePipelineResults
buildCombMatrixbuildCombMatrix
checkPipelinePackagescheckPipelinePackages
Correlations across clustering evaluation metricsclustMetricsCorr
colCenterScalecolCenterScale
Lists of control genesctrlgenes
dea_evalPlot_curvedea_evalPlot_curve
dea_pipelinedea_pipeline
defaultStepAggregationdefaultStepAggregation
evalHeatmapevalHeatmap
evaluateClusteringevaluateClustering
evaluateDEAevaluateDEA
evaluateDimRedevaluateDimRed
evaluateNormevaluateNorm
Example results from the DEA pipelineexampleDEAresults
Example pipeline resultsexampleResults
farthestPointfarthestPoint
getDimensionalitygetDimensionality
getQualitativePalettegetQualitativePalette
match_evaluate_multiplematch_evaluate_multiple
mergePipelineResultsmergePipelineResults
mockPipelinemockPipeline
parsePipNamesparsePipNames
PipelineDefinitionPipelineDefinition 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
plotElapsedplotElapsed
readPipelineResultsreadPipelineResults
runPipelinerunPipeline
scrna_describeDatasetsscrna_describeDatasets
scrna_evalPlot_filteringscrna_evalPlot_filtering
scrna_evalPlot_overallscrna_evalPlot_overall
scrna_evalPlot_silhscrna_evalPlot_silh
scrna_pipelinescrna_pipeline
Lists of stable genesstableG