CytoPipeline-class      CytoPipeline class
CytoProcessingStep      Cyto Processing step
OMIP021Samples          OMIP021Samples dataset
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
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).
estimateScaleTransforms
                        estimates scale tranformations
execute                 executing CytoPipeline object
exportCytoPipeline      exporting CytoPipeline objects
findTimeChannel         find time channel in flowSet/flowFrame
getAcquiredCompensationMatrix
                        extract compensation matrix from a
                        flowCore::flowFrame
getChannelNamesFromMarkers
                        get channel names from markers
getFCSFileName          get fcs file name
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
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
resetCellIDs            reset 'Original_ID' column in a flowframe
runCompensation         compensate with additional options
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
