# pipeComp pipeline benchmarking framework

## Documentation for package ‘pipeComp’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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