Package: pipeComp 1.17.0

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]

pipeComp_1.17.0.tar.gz
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pipeComp.pdf |pipeComp.html
pipeComp/json (API)
NEWS

# Install 'pipeComp' in R:
install.packages('pipeComp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Datasets:

On BioConductor:pipeComp-1.17.0(bioc 3.21)pipeComp-1.16.0(bioc 3.20)

geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq

7.01 score 40 stars 43 scripts 168 downloads 1 mentions 33 exports 209 dependencies

Last updated 25 days agofrom:be750efb4d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:addPipelineStepaggregatePipelineResultsargumentsbuildCombMatrixcheckPipelinePackagescolCenterScaledea_evalPlot_curvedea_pipelinedefaultArgumentsdefaultArguments<-defaultStepAggregationevalHeatmapevaluateClusteringevaluateDEAevaluateDimRedevaluateNormfarthestPointgetQualitativePalettematch_evaluate_multiplemergePipelineResultsmockPipelineparsePipNamesPipelineDefinitionplotElapsedreadPipelineResultsrunPipelinescrna_describeDatasetsscrna_evalPlot_filteringscrna_evalPlot_overallscrna_evalPlot_silhscrna_pipelinestepFnstepFn<-

Dependencies:abindaricodeaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphintrinsicDimensionIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6raggrandomcoloRRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotV8vctrsviporviridisviridisLitewithrxfunxtableXVectoryaImputeyamlzlibbioczoo

The pipeComp framework

Rendered frompipeComp.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

The DEA PipelineDefinition

Rendered frompipeComp_dea.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

The scRNA PipelineDefinition

Rendered frompipeComp_scRNA.Rmdusingknitr::rmarkdownon Oct 31 2024.

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