Man pages for DillonHammill/CytoExploreR
Interactive Analysis of Cytometry Data

cyto_applyApply a function over cytometry objects
cyto_barcodeBarcode each file in a flowSet with a sample ID
cyto_beads_sampleSample GatingSet to bead count
cyto_calibrateCalibrate channel ranges for cyto_plot
cyto_calibrate_resetRemove current calibration settings
cyto_channel_matchTable Editor for Channel Match File Construction
cyto_channelsExtract channel names
cyto_channel_selectSelect Fluorescent Channel for Compensation Controls
cyto_channels_extractExtract channels associated with certain markers
cyto_channels_restrictRestrict the channels of a cytometry object
cyto_checkCheck a flowFrame, flowSet, GatingHierarchy or GatingSet has...
cyto_cleanApply flowAI anomaly detection to clean cytometry data
cyto_compensateApply fluorescence compensation to samples
cyto_convertConvert between cytometry objects
cyto_copyCopy a cytoset, cytoframe or GatingSet
cyto_detailsExtract experiment details
cyto_details_editInteractively edit cyto_details for a flowSet or GatingSet
cyto_details_saveSave experiment details to csv file
cyto_emptyConstruct an empty flowFrame
cyto_exportExport cytometry data for use in flowJo or Cytobank
cyto_extractExtract a valid flowFrame or flowSet
cyto_filterFilter samples based on experiment variables
cyto_fluor_channelsExtract Fluorescent Channels
cyto_gate_boolAdd boolean gate to GatingSet and gatingTemplate
cyto_gate_convertConvert Between 1D and 2D Gate Objects
cyto_gate_drawInteractively draw and construct gate objects
cyto_gate_editEdit Existing Gate(s).
cyto_gate_extractExtract Saved Gate(s) from gatingTemplate.
cyto_gate_removeRemove Gate(s) and Edit gatingTemplate csv File
cyto_gate_renameRename Gates
cyto_gate_transformTransform gates objects
cyto_gate_typeGet Gate Type from Saved Gate.
cyto_gatingTemplate_activeActive gatingTemplate
cyto_gatingTemplate_applyApply gates saved in gatingTemplate to a GatingHierarchy or...
cyto_gatingTemplate_createCreate an empty gatingTemplate csv file
cyto_gatingTemplate_editInteractively Edit a gatingTemplate
cyto_gatingTemplate_generateGenerate a CytoExploreR gatingTemplate for a GatingHierarchy...
cyto_gatingTemplate_readRead in a gatingTemplate object or gatingTemplate csv file
cyto_gatingTemplate_selectSelect a gatingTemplate for downstream analyses
cyto_gatingTemplate_updateConvert CytoRSuite gatingTemplate to be compatible with...
cyto_gatingTemplate_writeWrite gatingTemplate to csv file
cyto_group_byGroup a flowSet or GatingSet by experiment variables
cyto_loadLoad .fcs files into ncdfFlowSet
cyto_mapCreate dimension-reduced maps of cytometry data
cyto_markersExtract marker names
cyto_markers_editAssign marker names to flowFrame or flowSet
cyto_markers_extractExtract marker names for certain channels
cyto_merge_byMerge a flowSet by experiment variables
cyto_namesExtract sample names
cyto_names_parseParse file names into experiment details
cyto_names-setReplacement method for cyto_names
cyto_nodesExtract Names of Gated Populations in GatingHierarchy or...
cyto_nodes_ancestorGet name of most recent common ancestor shared by nodes
cyto_nodes_convertConvert to unique node paths
cyto_plotcyto_plot
cyto_plot_compensationVisualise Compensation of Fluorescent Spillover in All...
cyto_plot_completeIndicate Completion of Custom cyto_plot Layout for Saving
cyto_plot_contourAdd contour lines to cyto_plot
cyto_plot_customCreate custom cyto_plot
cyto_plot_densityAdd density distributions to empty plots
cyto_plot_emptyCreate an empty cyto_plot
cyto_plot_exploreExplore Cytometry Data in Bivariate Plots
cyto_plot_gatePlot Gate Objects onto an Existing cyto_plot
cyto_plot_gating_schemePlot Cytometry Gating Strategies
cyto_plot_gating_treePlot Gating Trees
cyto_plot_labelAdd labels to cyto_plot
cyto_plot_labellerAdd labels to existing cyto_plot
cyto_plot_layoutSet Panel Layout for cyto_plot
cyto_plot_newOpen new graphics device for cyto_plot
cyto_plot_pointAdd points and contour lines to empty cyto_plot
cyto_plot_profilePlot expression profile in all channels
cyto_plot_recordRecord an existing cyto_plot
cyto_plot_resetReset all cyto_plot related settings
cyto_plot_saveSave High Resolution cyto_plot Images
cyto_plot_save_resetRevert unwanted cyto_plot_save call
cyto_plot_themeCreate custom themes for cyto_plot
cyto_plot_theme_argsGet supported cyto_plot_theme arguments
cyto_plot_theme_resetReset cyto_plot_theme to default settings
cyto_sampleSample a flowFrame or flowSet
cyto_saveWrite samples to FCS files in new folder or save GatingSet
cyto_selectSelect samples based on experiment variables
cyto_setupLoad.fcs files into GatingSet and annotate with experiment...
cyto_spillover_computeCompute Spillover Matrix
cyto_spillover_editInteractively Edit Spillover Matrices in Real-Time
cyto_spillover_extractExtract spillover matrix from cytometry object
cyto_spillover_spread_computeCompute Spillover Spreading Matrix
cyto_splitSplit samples merged with cyto_merge
cyto_stats_computeCompute, export and save statistics
cyto_transformApply Transformations to Cytometry Data
cyto_transformer_arcsinhDefinition(s) of arcsinh transformation(s)
cyto_transformer_biexDefinition(s) of biexponential transformation(s)
cyto_transformer_combineCombine cyto_transformer definitions
cyto_transformer_extractExtract transformers from a GatingHierarchy or GatingSet
cyto_transformer_logDefinition(s) of Log Transformation(s)
cyto_transformer_logicleDefinition(s) of logicle transformation(s)
cyto_transform_extractExtract Transformations from TransformerList
data_editorInteractive data editor
fftRtsneFIt-SNE Based on Kluger Lab FIt-SNE
file_ext_appendAppend file name with an extension
file_wd_checkCheck if a file exists in the current working directory
DillonHammill/CytoExploreR documentation built on July 9, 2020, 1:53 a.m.