Package: pipeComp 1.23.5

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_1.23.5.tar.gz
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pipeComp_1.23.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
pipeComp/json (API)

# 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

Datasets:

On BioConductor:pipeComp-1.23.2(bioc 3.24)pipeComp-1.22.1(bioc 3.23)

geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq

7.56 score 44 stars 46 scripts 339 downloads 1 mentions 33 exports 204 dependencies

Last updated from:35be0e31a9. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING271
linux-devel-x86_64NOTE587
source / vignettesOK384
linux-release-x86_64NOTE547
macos-release-arm64NOTE313
macos-oldrel-arm64NOTE270
windows-develNOTE447
windows-releaseNOTE417
windows-oldrelNOTE459
wasm-releaseOK197

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 scRNA PipelineDefinition
Introduction | The PipelineDefinition | Example run | Exploring the metrics | Doublet detection and cell filtering | Evaluation based on the reduced space | Subpopulation silhouette | Variance in the PCs explained by the subpopulations | Correlation with covariates | Clustering | Metrics | Plotting | Computing time | Extension and reuse | Datasets | scRNAseq benchmark datasets used in the paper | Using new datasets

Last update: 2026-05-26
Started: 2020-03-05

The pipeComp framework
Introduction | Installation | pipeComp overview | Running only a subset of the combinations | Dealing with the PipelineDefinition object | Creating a PipelineDefinition | Manipulating a PipelineDefinition | Merging results of different runPipeline calls | Handling errors | Debugging | Skipping errors and fixing them afterwards | Plotting results | Running times

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

The DEA PipelineDefinition
Introduction | Building the PipelineDefinition object | Preparing evaluation function | Assembling the PipelineDefinition | Example run | Building the wrappers | Defining the alternative parameter values to test | Benchmark datasets | Running the benchmark | Exploring the results

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

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