pipeComp pipeline benchmarking framework


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Documentation for package ‘pipeComp’ version 1.12.0

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pipeComp-package pipeComp - a framework for pipeline benchmarking
$-method Methods for 'PipelineDefinition' class
addPipelineStep addPipelineStep
aggregatePipelineResults aggregatePipelineResults
arguments Methods for 'PipelineDefinition' class
arguments-method Methods for 'PipelineDefinition' class
as.list-method Methods for 'PipelineDefinition' class
buildCombMatrix buildCombMatrix
checkPipelinePackages checkPipelinePackages
clustMetricsCorr Correlations across clustering evaluation metrics
colCenterScale colCenterScale
ctrlgenes Lists of control genes
dea_evalPlot_curve dea_evalPlot_curve
dea_pipeline dea_pipeline
defaultArguments Methods for 'PipelineDefinition' class
defaultArguments-method Methods for 'PipelineDefinition' class
defaultArguments<- Methods for 'PipelineDefinition' class
defaultArguments<--method Methods for 'PipelineDefinition' class
defaultStepAggregation defaultStepAggregation
evalHeatmap evalHeatmap
evaluateClustering evaluateClustering
evaluateDEA evaluateDEA
evaluateDimRed evaluateDimRed
evaluateNorm evaluateNorm
exampleDEAresults Example results from the DEA pipeline
exampleResults Example pipeline results
farthestPoint farthestPoint
getDimensionality getDimensionality
getQualitativePalette getQualitativePalette
length-method Methods for 'PipelineDefinition' class
match_evaluate_multiple match_evaluate_multiple
mergePipelineResults mergePipelineResults
mockPipeline mockPipeline
names-method Methods for 'PipelineDefinition' class
names<--method Methods for 'PipelineDefinition' class
parsePipNames parsePipNames
pipeComp pipeComp - a framework for pipeline benchmarking
PipelineDefinition PipelineDefinition
PipelineDefinition-class PipelineDefinition
PipelineDefinition-method Methods for 'PipelineDefinition' class
PipelineDefinition-methods Methods for 'PipelineDefinition' class
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
show-method Methods for 'PipelineDefinition' class
stableG Lists of stable genes
stepFn Methods for 'PipelineDefinition' class
stepFn-method Methods for 'PipelineDefinition' class
stepFn<- Methods for 'PipelineDefinition' class
stepFn<--method Methods for 'PipelineDefinition' class
[-method Methods for 'PipelineDefinition' class