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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(GetColorMap,AzimuthData)
S3method(GetColorMap,Seurat)
S3method(GetPlotRef,AzimuthData)
S3method(GetPlotRef,Seurat)
S3method(ReferenceVersion,AzimuthData)
S3method(ReferenceVersion,Seurat)
S3method(RunAzimuth,Seurat)
S3method(RunAzimuth,character)
S3method(RunAzimuthATAC,Seurat)
S3method(RunAzimuthATAC,character)
S3method(SetColorMap,AzimuthData)
S3method(SetColorMap,Seurat)
export(AzimuthApp)
export(AzimuthBridgeReference)
export(AzimuthReference)
export(Connect)
export(ConvertGeneNames)
export(CreateAzimuthData)
export(CreateColorMap)
export(GetColorMap)
export(GetPlotRef)
export(LoadBridgeReference)
export(LoadFileInput)
export(LoadH5ADobs)
export(LoadReference)
export(ReferenceVersion)
export(RunAzimuth)
export(RunAzimuthATAC)
export(SaveAzimuthReference)
export(SetColorMap)
export(ValidateAzimuthReference)
exportClasses(AzimuthData)
import(BSgenome.Hsapiens.UCSC.hg38)
importFrom(BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38)
importFrom(BiocGenerics,width)
importFrom(DT,DTOutput)
importFrom(DT,dataTableProxy)
importFrom(DT,renderDT)
importFrom(DT,selectRows)
importFrom(EnsDb.Hsapiens.v86,EnsDb.Hsapiens.v86)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,standardChromosomes)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(IRanges,findOverlaps)
importFrom(JASPAR2020,JASPAR2020)
importFrom(Matrix,sparse.model.matrix)
importFrom(Matrix,sparseMatrix)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(Seurat,Assays)
importFrom(Seurat,AverageExpression)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,DietSeurat)
importFrom(Seurat,DimPlot)
importFrom(Seurat,FeaturePlot)
importFrom(Seurat,FindBridgeTransferAnchors)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindTransferAnchors)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,IntegrateEmbeddings)
importFrom(Seurat,LabelClusters)
importFrom(Seurat,LoadAnnoyIndex)
importFrom(Seurat,Loadings)
importFrom(Seurat,MapQuery)
importFrom(Seurat,MappingScore)
importFrom(Seurat,MinMax)
importFrom(Seurat,NoLegend)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,PercentageFeatureSet)
importFrom(Seurat,Read10X_h5)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Seurat,TransferData)
importFrom(Seurat,VlnPlot)
importFrom(Seurat,as.Seurat)
importFrom(Seurat,as.sparse)
importFrom(SeuratData,AvailableData)
importFrom(SeuratData,InstallData)
importFrom(SeuratData,InstalledData)
importFrom(SeuratData,LoadData)
importFrom(SeuratDisk,Connect)
importFrom(SeuratObject,"DefaultAssay<-")
importFrom(SeuratObject,"Idents<-")
importFrom(SeuratObject,"Loadings<-")
importFrom(SeuratObject,"Misc<-")
importFrom(SeuratObject,"Tool<-")
importFrom(SeuratObject,AddMetaData)
importFrom(SeuratObject,Assays)
importFrom(SeuratObject,Cells)
importFrom(SeuratObject,CheckDots)
importFrom(SeuratObject,CreateSeuratObject)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,FetchData)
importFrom(SeuratObject,GetAssayData)
importFrom(SeuratObject,Idents)
importFrom(SeuratObject,Indices)
importFrom(SeuratObject,Key)
importFrom(SeuratObject,Loadings)
importFrom(SeuratObject,Misc)
importFrom(SeuratObject,Reductions)
importFrom(SeuratObject,RenameAssays)
importFrom(SeuratObject,RenameCells)
importFrom(SeuratObject,SetAssayData)
importFrom(SeuratObject,Tool)
importFrom(SeuratObject,VariableFeatures)
importFrom(SeuratObject,as.Neighbor)
importFrom(Signac,AddMotifs)
importFrom(Signac,Annotation)
importFrom(Signac,CreateChromatinAssay)
importFrom(Signac,Extend)
importFrom(Signac,FeatureMatrix)
importFrom(Signac,FindMotifs)
importFrom(Signac,FindTopFeatures)
importFrom(Signac,Fragments)
importFrom(Signac,GRangesToString)
importFrom(Signac,GeneActivity)
importFrom(Signac,GetGRangesFromEnsDb)
importFrom(Signac,RunChromVAR)
importFrom(Signac,RunSVD)
importFrom(Signac,RunTFIDF)
importFrom(TFBSTools,getMatrixSet)
importFrom(data.table,as.data.table)
importFrom(future,future)
importFrom(future,plan)
importFrom(future,resolved)
importFrom(future,value)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer_scales)
importFrom(ggplot2,scale_colour_hue)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(googlesheets4,gs4_auth)
importFrom(googlesheets4,gs4_get)
importFrom(googlesheets4,sheet_append)
importFrom(hdf5r,H5File)
importFrom(hdf5r,h5attr)
importFrom(htmltools,HTML)
importFrom(htmltools,div)
importFrom(htmltools,h3)
importFrom(htmltools,h4)
importFrom(htmltools,includeCSS)
importFrom(htmltools,p)
importFrom(htmltools,tagList)
importFrom(htmltools,tags)
importFrom(httr,GET)
importFrom(httr,build_url)
importFrom(httr,parse_url)
importFrom(httr,status_code)
importFrom(httr,timeout)
importFrom(jsonlite,read_json)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(patchwork,wrap_plots)
importFrom(plotly,ggplotly)
importFrom(plotly,plot_ly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(plotly,toWebGL)
importFrom(presto,wilcoxauc)
importFrom(rhdf5,h5read)
importFrom(rlang,"%||%")
importFrom(scales,hue_pal)
importFrom(shiny,Progress)
importFrom(shiny,actionButton)
importFrom(shiny,checkboxGroupInput)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,fileInput)
importFrom(shiny,fluidRow)
importFrom(shiny,getDefaultReactiveDomain)
importFrom(shiny,hoverOpts)
importFrom(shiny,htmlOutput)
importFrom(shiny,icon)
importFrom(shiny,insertUI)
importFrom(shiny,isRunning)
importFrom(shiny,isolate)
importFrom(shiny,modalDialog)
importFrom(shiny,nearPoints)
importFrom(shiny,numericInput)
importFrom(shiny,observeEvent)
importFrom(shiny,onStop)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactiveValues)
importFrom(shiny,removeUI)
importFrom(shiny,renderPlot)
importFrom(shiny,renderTable)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,runApp)
importFrom(shiny,safeError)
importFrom(shiny,selectizeInput)
importFrom(shiny,setProgress)
importFrom(shiny,shinyApp)
importFrom(shiny,showModal)
importFrom(shiny,showNotification)
importFrom(shiny,tableOutput)
importFrom(shiny,textAreaInput)
importFrom(shiny,textOutput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateCheckboxInput)
importFrom(shiny,updateNumericInput)
importFrom(shiny,updateSelectizeInput)
importFrom(shiny,updateTextAreaInput)
importFrom(shiny,verbatimTextOutput)
importFrom(shiny,wellPanel)
importFrom(shiny,withProgress)
importFrom(shinyBS,bsButton)
importFrom(shinyBS,bsPopover)
importFrom(shinyBS,bsTooltip)
importFrom(shinydashboard,box)
importFrom(shinydashboard,dashboardBody)
importFrom(shinydashboard,dashboardHeader)
importFrom(shinydashboard,dashboardPage)
importFrom(shinydashboard,dashboardSidebar)
importFrom(shinydashboard,menuItem)
importFrom(shinydashboard,renderMenu)
importFrom(shinydashboard,renderValueBox)
importFrom(shinydashboard,sidebarMenu)
importFrom(shinydashboard,sidebarMenuOutput)
importFrom(shinydashboard,tabItem)
importFrom(shinydashboard,tabItems)
importFrom(shinydashboard,valueBox)
importFrom(shinydashboard,valueBoxOutput)
importFrom(shinyjs,addClass)
importFrom(shinyjs,disable)
importFrom(shinyjs,disabled)
importFrom(shinyjs,enable)
importFrom(shinyjs,hide)
importFrom(shinyjs,onclick)
importFrom(shinyjs,removeClass)
importFrom(shinyjs,show)
importFrom(shinyjs,useShinyjs)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stringr,str_interp)
importFrom(stringr,str_match)
importFrom(stringr,str_split)
importFrom(stringr,str_trim)
importFrom(tools,file_ext)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,write.table)
importFrom(withr,with_options)
useDynLib(Azimuth)