All functions |
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CytoPipeline package |
CytoPipeline class |
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Cyto Processing step |
OMIP021Samples dataset |
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Aggregate and sample multiple flow frames of a flow set together |
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append 'Original_ID' column to a flowframe |
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apply scale transforms |
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find flow frame columns that represent fluorochrome channel |
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find flow frame columns that represent true signal |
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compensation of fcs file(s) from matrix |
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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). |
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estimates scale tranformations |
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executing CytoPipeline object |
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exporting CytoPipeline objects |
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find time channel in flowSet/flowFrame |
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extract compensation matrix from a flowCore::flowFrame |
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get channel names from markers |
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get fcs file name |
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get tranformation parameters for a specific channel |
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plot events in 1D or 2D, using ggplot2 |
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plot filtered events in 2D, using ggplot |
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plot flow rate as a function of time, using ggplot2 |
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handling processing steps in CytoPipeline objects |
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inspect CytoPipeline results objects |
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interaction between CytoPipeline object and disk cache |
perform QC with flowAI |
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perform QC with PeacoQC |
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read RDS object |
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Read fcs sample files |
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remove channels from a flowFrame |
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remove dead cells from a flowFrame using manual gating |
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remove debris from a flowFrame using manual gating |
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remove doublets from a flowFrame, using CytoPipeline custom algorithm |
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remove margin events using PeacoQC |
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compensate with additional options |
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Clean doublet events from flow cytometry data |
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sub-sampling of a flowFrame |
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update marker name of a given flowFrame channel |
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write flowFrame to disk |