Package: pipeComp 1.17.0
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_1.17.0.tar.gz
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pipeComp_1.17.0.tgz(r-4.4-any)pipeComp_1.17.0.tgz(r-4.3-any)
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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')) |
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-1.17.0(bioc 3.21)pipeComp-1.16.0(bioc 3.20)
geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq
Last updated 25 days agofrom:be750efb4d. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-win | NOTE | Oct 31 2024 |
R-4.5-linux | NOTE | Oct 31 2024 |
R-4.4-win | NOTE | Oct 31 2024 |
R-4.4-mac | NOTE | Oct 31 2024 |
R-4.3-win | NOTE | Oct 31 2024 |
R-4.3-mac | NOTE | Oct 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.Rmd
usingknitr::rmarkdown
on Oct 31 2024.Last update: 2020-09-04
Started: 2020-03-05
The DEA PipelineDefinition
Rendered frompipeComp_dea.Rmd
usingknitr::rmarkdown
on Oct 31 2024.Last update: 2020-04-29
Started: 2020-04-20
The scRNA PipelineDefinition
Rendered frompipeComp_scRNA.Rmd
usingknitr::rmarkdown
on Oct 31 2024.Last update: 2020-07-23
Started: 2020-03-05
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 |