NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(cyto_channels_restrict,GatingSet)
S3method(cyto_channels_restrict,flowFrame)
S3method(cyto_channels_restrict,flowSet)
S3method(cyto_compensate,GatingSet)
S3method(cyto_compensate,flowFrame)
S3method(cyto_compensate,flowSet)
S3method(cyto_convert,GatingHierarchy)
S3method(cyto_convert,GatingSet)
S3method(cyto_convert,flowFrame)
S3method(cyto_convert,flowSet)
S3method(cyto_gate_convert,default)
S3method(cyto_gate_convert,ellipsoidGate)
S3method(cyto_gate_convert,filters)
S3method(cyto_gate_convert,list)
S3method(cyto_gate_convert,polygonGate)
S3method(cyto_gate_convert,quadGate)
S3method(cyto_gate_convert,rectangleGate)
S3method(cyto_gate_draw,GatingSet)
S3method(cyto_gate_draw,flowFrame)
S3method(cyto_gate_draw,flowSet)
S3method(cyto_gate_transform,ellipsoidGate)
S3method(cyto_gate_transform,filters)
S3method(cyto_gate_transform,list)
S3method(cyto_gate_transform,polygonGate)
S3method(cyto_gate_transform,quadGate)
S3method(cyto_gate_transform,rectangleGate)
S3method(cyto_gatingTemplate_generate,GatingHierarchy)
S3method(cyto_gatingTemplate_generate,GatingSet)
S3method(cyto_map,GatingSet)
S3method(cyto_map,flowFrame)
S3method(cyto_map,flowSet)
S3method(cyto_markers,GatingHierarchy)
S3method(cyto_markers,GatingSet)
S3method(cyto_markers,flowFrame)
S3method(cyto_markers,flowSet)
S3method(cyto_merge_by,GatingSet)
S3method(cyto_merge_by,flowSet)
S3method(cyto_names,GatingHierarchy)
S3method(cyto_names,GatingSet)
S3method(cyto_names,flowFrame)
S3method(cyto_names,flowSet)
S3method(cyto_names,list)
S3method(cyto_plot,GatingHierarchy)
S3method(cyto_plot,GatingSet)
S3method(cyto_plot,flowFrame)
S3method(cyto_plot,flowSet)
S3method(cyto_plot_compensation,GatingHierarchy)
S3method(cyto_plot_compensation,GatingSet)
S3method(cyto_plot_compensation,flowFrame)
S3method(cyto_plot_compensation,flowSet)
S3method(cyto_plot_contour,flowFrame)
S3method(cyto_plot_contour,flowSet)
S3method(cyto_plot_contour,list)
S3method(cyto_plot_density,flowFrame)
S3method(cyto_plot_density,list)
S3method(cyto_plot_empty,flowFrame)
S3method(cyto_plot_empty,list)
S3method(cyto_plot_explore,GatingHierarchy)
S3method(cyto_plot_explore,GatingSet)
S3method(cyto_plot_explore,flowFrame)
S3method(cyto_plot_explore,flowSet)
S3method(cyto_plot_gate,default)
S3method(cyto_plot_gate,ellipsoidGate)
S3method(cyto_plot_gate,filters)
S3method(cyto_plot_gate,list)
S3method(cyto_plot_gate,polygonGate)
S3method(cyto_plot_gate,quadGate)
S3method(cyto_plot_gate,rectangleGate)
S3method(cyto_plot_gating_scheme,GatingHierarchy)
S3method(cyto_plot_gating_scheme,GatingSet)
S3method(cyto_plot_gating_tree,GatingHierarchy)
S3method(cyto_plot_gating_tree,GatingSet)
S3method(cyto_plot_gating_tree,gatingTemplate)
S3method(cyto_plot_label,GatingHierarchy)
S3method(cyto_plot_label,flowFrame)
S3method(cyto_plot_point,flowFrame)
S3method(cyto_plot_point,list)
S3method(cyto_plot_profile,GatingHierarchy)
S3method(cyto_plot_profile,GatingSet)
S3method(cyto_plot_profile,flowFrame)
S3method(cyto_plot_profile,flowSet)
S3method(cyto_sample,GatingHierarchy)
S3method(cyto_sample,GatingSet)
S3method(cyto_sample,flowFrame)
S3method(cyto_sample,flowSet)
S3method(cyto_sample,list)
S3method(cyto_save,GatingHierarchy)
S3method(cyto_save,GatingSet)
S3method(cyto_save,flowFrame)
S3method(cyto_save,flowSet)
S3method(cyto_spillover_edit,GatingSet)
S3method(cyto_spillover_edit,flowSet)
S3method(cyto_stats_compute,GatingHierarchy)
S3method(cyto_stats_compute,GatingSet)
S3method(cyto_stats_compute,flowFrame)
S3method(cyto_stats_compute,flowSet)
S3method(cyto_transform,default)
S3method(cyto_transform,transformList)
S3method(cyto_transform,transformerList)
S3method(cyto_transformer_arcsinh,GatingHierarchy)
S3method(cyto_transformer_arcsinh,GatingSet)
S3method(cyto_transformer_arcsinh,flowFrame)
S3method(cyto_transformer_arcsinh,flowSet)
S3method(cyto_transformer_biex,GatingHierarchy)
S3method(cyto_transformer_biex,GatingSet)
S3method(cyto_transformer_biex,flowFrame)
S3method(cyto_transformer_biex,flowSet)
S3method(cyto_transformer_log,GatingHierarchy)
S3method(cyto_transformer_log,GatingSet)
S3method(cyto_transformer_log,flowFrame)
S3method(cyto_transformer_log,flowSet)
S3method(cyto_transformer_logicle,GatingHierarchy)
S3method(cyto_transformer_logicle,GatingSet)
S3method(cyto_transformer_logicle,flowFrame)
S3method(cyto_transformer_logicle,flowSet)
export("cyto_details<-")
export("cyto_names<-")
export(cyto_apply)
export(cyto_barcode)
export(cyto_beads_sample)
export(cyto_calibrate)
export(cyto_calibrate_reset)
export(cyto_channel_match)
export(cyto_channel_select)
export(cyto_channels)
export(cyto_channels_extract)
export(cyto_channels_restrict)
export(cyto_check)
export(cyto_clean)
export(cyto_compensate)
export(cyto_convert)
export(cyto_copy)
export(cyto_details)
export(cyto_details_edit)
export(cyto_details_save)
export(cyto_empty)
export(cyto_export)
export(cyto_extract)
export(cyto_filter)
export(cyto_fluor_channels)
export(cyto_gate_bool)
export(cyto_gate_convert)
export(cyto_gate_copy)
export(cyto_gate_draw)
export(cyto_gate_edit)
export(cyto_gate_extract)
export(cyto_gate_remove)
export(cyto_gate_rename)
export(cyto_gate_transform)
export(cyto_gate_type)
export(cyto_gatingTemplate_active)
export(cyto_gatingTemplate_apply)
export(cyto_gatingTemplate_create)
export(cyto_gatingTemplate_edit)
export(cyto_gatingTemplate_generate)
export(cyto_gatingTemplate_read)
export(cyto_gatingTemplate_select)
export(cyto_gatingTemplate_update)
export(cyto_gatingTemplate_write)
export(cyto_group_by)
export(cyto_load)
export(cyto_map)
export(cyto_markers)
export(cyto_markers_edit)
export(cyto_markers_extract)
export(cyto_merge_by)
export(cyto_names)
export(cyto_names_parse)
export(cyto_nodes)
export(cyto_nodes_ancestor)
export(cyto_nodes_convert)
export(cyto_plot)
export(cyto_plot_compensation)
export(cyto_plot_complete)
export(cyto_plot_contour)
export(cyto_plot_custom)
export(cyto_plot_density)
export(cyto_plot_empty)
export(cyto_plot_explore)
export(cyto_plot_gate)
export(cyto_plot_gating_scheme)
export(cyto_plot_gating_tree)
export(cyto_plot_label)
export(cyto_plot_labeller)
export(cyto_plot_layout)
export(cyto_plot_new)
export(cyto_plot_point)
export(cyto_plot_profile)
export(cyto_plot_record)
export(cyto_plot_reset)
export(cyto_plot_save)
export(cyto_plot_save_reset)
export(cyto_plot_theme)
export(cyto_plot_theme_args)
export(cyto_plot_theme_reset)
export(cyto_sample)
export(cyto_save)
export(cyto_select)
export(cyto_setup)
export(cyto_spillover_compute)
export(cyto_spillover_edit)
export(cyto_spillover_extract)
export(cyto_spillover_spread_compute)
export(cyto_split)
export(cyto_stats_compute)
export(cyto_transform)
export(cyto_transform_extract)
export(cyto_transformer_arcsinh)
export(cyto_transformer_biex)
export(cyto_transformer_combine)
export(cyto_transformer_extract)
export(cyto_transformer_log)
export(cyto_transformer_logicle)
export(data_editor)
export(fftRtsne)
export(file_wd_check)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,nrow)
importFrom(EmbedSOM,EmbedSOM)
importFrom(EmbedSOM,SOM)
importFrom(MASS,kde2d)
importFrom(Rtsne,Rtsne)
importFrom(bslib,bs_theme)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,select)
importFrom(flowAI,flow_auto_qc)
importFrom(flowCore,"identifier<-")
importFrom(flowCore,"pData<-")
importFrom(flowCore,"parameters<-")
importFrom(flowCore,"phenoData<-")
importFrom(flowCore,CytoExploreR_.estimateLogicle)
importFrom(flowCore,Subset)
importFrom(flowCore,`identifier<-`)
importFrom(flowCore,compensate)
importFrom(flowCore,decompensate)
importFrom(flowCore,each_col)
importFrom(flowCore,ellipsoidGate)
importFrom(flowCore,exprs)
importFrom(flowCore,filterList)
importFrom(flowCore,filters)
importFrom(flowCore,flowFrame)
importFrom(flowCore,flowSet)
importFrom(flowCore,fr_append_cols)
importFrom(flowCore,fsApply)
importFrom(flowCore,identifier)
importFrom(flowCore,inverseLogicleTransform)
importFrom(flowCore,keyword)
importFrom(flowCore,parameters)
importFrom(flowCore,phenoData)
importFrom(flowCore,polygonGate)
importFrom(flowCore,quadGate)
importFrom(flowCore,rectangleGate)
importFrom(flowCore,sampleFilter)
importFrom(flowCore,sampleNames)
importFrom(flowCore,split)
importFrom(flowCore,transform)
importFrom(flowCore,transformList)
importFrom(flowCore,write.FCS)
importFrom(flowWorkspace,"gs_cyto_data<-")
importFrom(flowWorkspace,"pData<-")
importFrom(flowWorkspace,"sampleNames<-")
importFrom(flowWorkspace,GatingSet)
importFrom(flowWorkspace,`sampleNames<-`)
importFrom(flowWorkspace,asinh_Gml2)
importFrom(flowWorkspace,booleanFilter)
importFrom(flowWorkspace,cf_append_cols)
importFrom(flowWorkspace,cytoset)
importFrom(flowWorkspace,cytoset_to_flowSet)
importFrom(flowWorkspace,flowFrame_to_cytoframe)
importFrom(flowWorkspace,flowSet_to_cytoset)
importFrom(flowWorkspace,flow_trans)
importFrom(flowWorkspace,flowjo_biexp)
importFrom(flowWorkspace,flowjo_log_trans)
importFrom(flowWorkspace,gh_get_compensations)
importFrom(flowWorkspace,gh_get_pop_paths)
importFrom(flowWorkspace,gh_get_transformations)
importFrom(flowWorkspace,gh_pop_get_children)
importFrom(flowWorkspace,gh_pop_get_data)
importFrom(flowWorkspace,gh_pop_get_descendants)
importFrom(flowWorkspace,gh_pop_get_gate)
importFrom(flowWorkspace,gh_pop_get_parent)
importFrom(flowWorkspace,gh_pop_is_negated)
importFrom(flowWorkspace,gh_pop_set_gate)
importFrom(flowWorkspace,gh_pop_set_name)
importFrom(flowWorkspace,gs_clone)
importFrom(flowWorkspace,gs_cyto_data)
importFrom(flowWorkspace,gs_get_compensations)
importFrom(flowWorkspace,gs_get_pop_paths)
importFrom(flowWorkspace,gs_pop_add)
importFrom(flowWorkspace,gs_pop_get_children)
importFrom(flowWorkspace,gs_pop_get_data)
importFrom(flowWorkspace,gs_pop_get_gate)
importFrom(flowWorkspace,gs_pop_remove)
importFrom(flowWorkspace,gs_pop_set_gate)
importFrom(flowWorkspace,gs_pop_set_name)
importFrom(flowWorkspace,load_cytoset_from_fcs)
importFrom(flowWorkspace,load_gs)
importFrom(flowWorkspace,pData)
importFrom(flowWorkspace,realize_view)
importFrom(flowWorkspace,recompute)
importFrom(flowWorkspace,sampleNames)
importFrom(flowWorkspace,save_gs)
importFrom(flowWorkspace,transformerList)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRamp)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,densCols)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,dev.size)
importFrom(grDevices,graphics.off)
importFrom(grDevices,jpeg)
importFrom(grDevices,n2mfrow)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,recordPlot)
importFrom(grDevices,rgb)
importFrom(grDevices,svg)
importFrom(grDevices,tiff)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,contour)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,locator)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rasterImage)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,formalArgs)
importFrom(methods,is)
importFrom(openCyto,CytoExploreR_.argDeparser)
importFrom(openCyto,CytoExploreR_.preprocess_csv)
importFrom(openCyto,gatingTemplate)
importFrom(openCyto,gh_generate_template)
importFrom(openCyto,gs_add_gating_method)
importFrom(openCyto,gt_gating)
importFrom(openCyto,gt_get_gate)
importFrom(openCyto,gt_get_nodes)
importFrom(openCyto,registerPlugins)
importFrom(purrr,transpose)
importFrom(rhandsontable,hot_col)
importFrom(rhandsontable,hot_cols)
importFrom(rhandsontable,hot_rows)
importFrom(rhandsontable,hot_to_r)
importFrom(rhandsontable,rHandsontableOutput)
importFrom(rhandsontable,renderRHandsontable)
importFrom(rhandsontable,rhandsontable)
importFrom(robustbase,colMedians)
importFrom(rsvd,rpca)
importFrom(rsvd,rsvd)
importFrom(shiny,actionButton)
importFrom(shiny,checkboxInput)
importFrom(shiny,div)
importFrom(shiny,eventReactive)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,img)
importFrom(shiny,mainPanel)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,onStop)
importFrom(shiny,paneViewer)
importFrom(shiny,plotOutput)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderPlot)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,stopApp)
importFrom(shiny,tabPanel)
importFrom(shiny,tabsetPanel)
importFrom(shiny,titlePanel)
importFrom(shiny,updateCheckboxInput)
importFrom(shiny,updateSelectInput)
importFrom(stats,bw.nrd0)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(tibble,add_column)
importFrom(tibble,as_tibble)
importFrom(tibble,remove_rownames)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(umap,umap)
importFrom(utils,capture.output)
importFrom(utils,edit)
importFrom(utils,file_test)
importFrom(utils,menu)
importFrom(utils,modifyList)
importFrom(utils,read.csv)
importFrom(utils,select.list)
importFrom(utils,write.csv)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visNetwork)