Automation and visualization of flow cytometry data analysis pipelines

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Documentation for package ‘CytoPipeline’ version 1.9.0

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

Help Pages

addProcessingStep	handling processing steps in CytoPipeline objects
aggregateAndSample	Aggregate and sample multiple flow frames of a flow set together
appendCellID	append 'Original_ID' column to a flowframe
applyScaleTransforms	apply scale transforms
areFluoCols	find flow frame columns that represent fluorochrome channel
areSignalCols	find flow frame columns that represent true signal
as.json.CytoProcessingStep	Cyto Processing step
as.list.CytoPipeline	CytoPipeline class
as.list.CytoProcessingStep	Cyto Processing step
buildCytoPipelineFromCache	interaction between CytoPipeline object and disk cache
characterOrFunction-class	Cyto Processing step
checkCytoPipelineConsistencyWithCache	interaction between CytoPipeline object and disk cache
cleanProcessingSteps	handling processing steps in CytoPipeline objects
collectNbOfRetainedEvents	inspect CytoPipeline results objects
compensateFromMatrix	compensation of fcs file(s) from matrix
computeScatterChannelsLinearScale	compute linear transformation of scatter channels found in ff, based on 5% and 95% of referenceChannel, set as target. If there is a transformation defined in transList for referenceChannel, it is applied first, before computing quantiles. Then the computed linear transformations (or each scatter channel) are added into the transfo_list. -A channels are computed, and same linear transformation is then applied to corresponding -W and -H channels (if they exist in ff).
CytoPipeline-class	CytoPipeline class
CytoPipeline-class,	CytoPipeline class
CytoPipeline-method	CytoPipeline class
CytoPipelineClass	CytoPipeline class
CytoProcessingStep	Cyto Processing step
CytoProcessingStep-class	Cyto Processing step
deleteCytoPipelineCache	interaction between CytoPipeline object and disk cache
estimateScaleTransforms	estimates scale tranformations
execute	executing CytoPipeline object
executeProcessingStep	Cyto Processing step
experimentName	CytoPipeline class
experimentName<-	CytoPipeline class
export2JSONFile	exporting CytoPipeline objects
exportCytoPipeline	exporting CytoPipeline objects
findTimeChannel	find time channel in flowSet/flowFrame
from.json.CytoProcessingStep	Cyto Processing step
getAcquiredCompensationMatrix	extract compensation matrix from a flowCore::flowFrame
getChannelNamesFromMarkers	get channel names from markers
getCPSARGS	Cyto Processing step
getCPSFUN	Cyto Processing step
getCPSName	Cyto Processing step
getCytoPipelineExperimentNames	inspect CytoPipeline results objects
getCytoPipelineFlowFrame	inspect CytoPipeline results objects
getCytoPipelineObjectFromCache	inspect CytoPipeline results objects
getCytoPipelineObjectInfos	inspect CytoPipeline results objects
getCytoPipelineScaleTransform	inspect CytoPipeline results objects
getFCSFileName	get fcs file name
getNbProcessingSteps	handling processing steps in CytoPipeline objects
getProcessingStep	handling processing steps in CytoPipeline objects
getProcessingStepNames	handling processing steps in CytoPipeline objects
getTransfoParams	get tranformation parameters for a specific channel
ggplotEvents	plot events in 1D or 2D, using ggplot2
ggplotFilterEvents	plot filtered events in 2D, using ggplot
ggplotFlowRate	plot flow rate as a function of time, using ggplot2
handlingProcessingSteps	handling processing steps in CytoPipeline objects
inspectCytoPipelineObjects	inspect CytoPipeline results objects
interactingWithCytoPipelineCache	interaction between CytoPipeline object and disk cache
OMIP021Samples	OMIP021Samples dataset
pData	CytoPipeline class
pData<-	CytoPipeline class
plotCytoPipelineProcessingQueue	inspect CytoPipeline results objects
qualityControlFlowAI	perform QC with flowAI
qualityControlPeacoQC	perform QC with PeacoQC
readRDSObject	read RDS object
readSampleFiles	Read fcs sample files
removeChannels	remove channels from a flowFrame
removeDeadCellsManualGate	remove dead cells from a flowFrame using manual gating
removeDebrisManualGate	remove debris from a flowFrame using manual gating
removeDoubletsCytoPipeline	remove doublets from a flowFrame, using CytoPipeline custom algorithm
removeMarginsPeacoQC	remove margin events using PeacoQC
removeProcessingStep	handling processing steps in CytoPipeline objects
resetCellIDs	reset 'Original_ID' column in a flowframe
runCompensation	compensate with additional options
sampleFiles	CytoPipeline class
sampleFiles<-	CytoPipeline class
show-method	CytoPipeline class
show-method	Cyto Processing step
showProcessingSteps	handling processing steps in CytoPipeline objects
singletsGate	Clean doublet events from flow cytometry data
subsample	sub-sampling of a flowFrame
updateMarkerName	update marker name of a given flowFrame channel
writeFlowFrame	write flowFrame to disk