--- a
+++ b/NAMESPACE
@@ -0,0 +1,331 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method("$",VoltRon)
+S3method("$<-",VoltRon)
+S3method(as.VoltRon,Seurat)
+S3method(as.VoltRon,SpatialExperiment)
+S3method(as.Zarr,"magick-image")
+export("vrCoordinates<-")
+export("vrEmbeddings<-")
+export("vrFeatureData<-")
+export("vrGraph<-")
+export("vrImages<-")
+export("vrMainAssay<-")
+export("vrMainChannel<-")
+export("vrMainFeatureType<-")
+export("vrMainImage<-")
+export("vrMainSpatial<-")
+export("vrSegments<-")
+export("vrSpatialPoints<-")
+export(FromSegmentToCrop)
+export(Metadata)
+export(SampleMetadata)
+export(addAssay)
+export(addFeature)
+export(addMetadata)
+export(addSpatialLayer)
+export(annotateSpatialData)
+export(as.AnnData)
+export(as.Giotto)
+export(as.OmeTiff)
+export(as.OmeZarr)
+export(as.Seurat)
+export(as.SpatialExperiment)
+export(as.VoltRon)
+export(as.Zarr)
+export(combineChannels)
+export(combineGraphs)
+export(convertAnnDataToVoltRon)
+export(flipCoordinates)
+export(formAssay)
+export(formImage)
+export(formVoltRon)
+export(generateCosMxImage)
+export(generateGeoJSON)
+export(generateSegments)
+export(generateTileData)
+export(generateXeniumImage)
+export(getBasilisk)
+export(getClusters)
+export(getDeconvolution)
+export(getDiffExp)
+export(getFeatures)
+export(getHotSpotAnalysis)
+export(getNicheAssay)
+export(getPCA)
+export(getProfileNeighbors)
+export(getRcppAutomatedRegistration)
+export(getRcppManualRegistration)
+export(getRcppWarpImage)
+export(getSpatialNeighbors)
+export(getUMAP)
+export(getVariableFeatures)
+export(import10Xh5)
+export(importCosMx)
+export(importDBITSeq)
+export(importGenePS)
+export(importGeoMx)
+export(importImageData)
+export(importOpenST)
+export(importPhenoCycler)
+export(importSTOmics)
+export(importVisium)
+export(importVisiumHD)
+export(importXenium)
+export(loadVoltRon)
+export(modulateImage)
+export(normalizeData)
+export(registerSpatialData)
+export(resizeImage)
+export(saveVoltRon)
+export(transferData)
+export(updateAssay)
+export(vrAssayNames)
+export(vrAssayParams)
+export(vrAssayTypes)
+export(vrBarPlot)
+export(vrCoordinates)
+export(vrData)
+export(vrEmbeddingFeaturePlot)
+export(vrEmbeddingNames)
+export(vrEmbeddingPlot)
+export(vrEmbeddings)
+export(vrFeatureData)
+export(vrFeatureTypeNames)
+export(vrFeatures)
+export(vrGraph)
+export(vrGraphNames)
+export(vrHeatmapPlot)
+export(vrImageChannelNames)
+export(vrImageNames)
+export(vrImages)
+export(vrMainAssay)
+export(vrMainChannel)
+export(vrMainFeatureType)
+export(vrMainImage)
+export(vrMainSpatial)
+export(vrNeighbourhoodEnrichment)
+export(vrNeighbourhoodEnrichmentPlot)
+export(vrProportionPlot)
+export(vrSampleNames)
+export(vrScatterPlot)
+export(vrSegments)
+export(vrSpatialFeaturePlot)
+export(vrSpatialNames)
+export(vrSpatialPlot)
+export(vrSpatialPoints)
+export(vrViolinPlot)
+exportClasses(VoltRon)
+exportClasses(vrAssay)
+exportClasses(vrAssayV2)
+exportClasses(vrBlock)
+exportClasses(vrImage)
+exportClasses(vrLayer)
+exportClasses(vrMetadata)
+exportClasses(vrSample)
+exportClasses(vrSpatial)
+exportMethods("Metadata<-")
+exportMethods("[[")
+exportMethods("[[<-")
+exportMethods("vrCoordinates<-")
+exportMethods("vrEmbeddings<-")
+exportMethods("vrFeatureData<-")
+exportMethods("vrImages<-")
+exportMethods("vrMainAssay<-")
+exportMethods("vrMainChannel<-")
+exportMethods("vrMainFeatureType<-")
+exportMethods("vrMainImage<-")
+exportMethods("vrMainSpatial<-")
+exportMethods("vrSegments<-")
+exportMethods("vrSpatialPoints<-")
+exportMethods(Metadata)
+exportMethods(addAssay)
+exportMethods(addFeature)
+exportMethods(combineChannels)
+exportMethods(flipCoordinates)
+exportMethods(generateTileData)
+exportMethods(getFeatures)
+exportMethods(merge)
+exportMethods(modulateImage)
+exportMethods(normalizeData)
+exportMethods(resizeImage)
+exportMethods(subset)
+exportMethods(updateAssay)
+exportMethods(vrAssayNames)
+exportMethods(vrAssayTypes)
+exportMethods(vrCoordinates)
+exportMethods(vrData)
+exportMethods(vrEmbeddingNames)
+exportMethods(vrEmbeddings)
+exportMethods(vrFeatureData)
+exportMethods(vrFeatureTypeNames)
+exportMethods(vrFeatures)
+exportMethods(vrImageChannelNames)
+exportMethods(vrImageNames)
+exportMethods(vrImages)
+exportMethods(vrMainAssay)
+exportMethods(vrMainChannel)
+exportMethods(vrMainFeatureType)
+exportMethods(vrMainImage)
+exportMethods(vrMainSpatial)
+exportMethods(vrSampleNames)
+exportMethods(vrSegments)
+exportMethods(vrSpatialNames)
+exportMethods(vrSpatialPoints)
+import(ggplot2)
+import(shiny)
+importClassesFrom(Matrix,dgCMatrix)
+importClassesFrom(Matrix,dgRMatrix)
+importClassesFrom(Matrix,dgeMatrix)
+importClassesFrom(S4Arrays,Array)
+importClassesFrom(data.table,data.table)
+importFrom(EBImage,as.Image)
+importFrom(EBImage,writeImage)
+importFrom(Matrix,Matrix)
+importFrom(Matrix,colSums)
+importFrom(Matrix,rowMeans)
+importFrom(Matrix,rowSums)
+importFrom(Matrix,sparseMatrix)
+importFrom(Matrix,t)
+importFrom(RANN,nn2)
+importFrom(RCDT,delaunay)
+importFrom(RcppAnnoy,AnnoyEuclidean)
+importFrom(data.table,alloc.col)
+importFrom(data.table,as.data.table)
+importFrom(data.table,chmatch)
+importFrom(data.table,data.table)
+importFrom(data.table,fread)
+importFrom(data.table,is.data.table)
+importFrom(data.table,melt)
+importFrom(data.table,set)
+importFrom(data.table,setkey)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,add_row)
+importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,coalesce)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_all)
+importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
+importFrom(dplyr,right_join)
+importFrom(dplyr,select)
+importFrom(dplyr,summarize)
+importFrom(dplyr,tibble)
+importFrom(ggplot2,annotation_custom)
+importFrom(ggplot2,annotation_raster)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,geom_rect)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggproto)
+importFrom(ggplot2,xlim)
+importFrom(ggplot2,ylim)
+importFrom(ggpubr,ggarrange)
+importFrom(ggrepel,geom_label_repel)
+importFrom(grDevices,as.raster)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,hcl)
+importFrom(grDevices,rgb)
+importFrom(grDevices,rgb2hsv)
+importFrom(grid,gpar)
+importFrom(grid,pointsGrob)
+importFrom(grid,rasterGrob)
+importFrom(grid,unit)
+importFrom(ids,random_id)
+importFrom(igraph,"E<-")
+importFrom(igraph,"V<-")
+importFrom(igraph,E)
+importFrom(igraph,V)
+importFrom(igraph,add_edges)
+importFrom(igraph,as_adjacency_matrix)
+importFrom(igraph,as_data_frame)
+importFrom(igraph,cluster_leiden)
+importFrom(igraph,components)
+importFrom(igraph,disjoint_union)
+importFrom(igraph,edge_attr_names)
+importFrom(igraph,get.data.frame)
+importFrom(igraph,graph_from_adjacency_matrix)
+importFrom(igraph,induced_subgraph)
+importFrom(igraph,make_empty_graph)
+importFrom(igraph,neighborhood)
+importFrom(igraph,simplify)
+importFrom(igraph,subgraph)
+importFrom(igraph,union)
+importFrom(igraph,vcount)
+importFrom(igraph,vertices)
+importFrom(irlba,irlba)
+importFrom(magick,geometry_size_percent)
+importFrom(magick,image_composite)
+importFrom(magick,image_contrast)
+importFrom(magick,image_crop)
+importFrom(magick,image_data)
+importFrom(magick,image_flip)
+importFrom(magick,image_flop)
+importFrom(magick,image_ggplot)
+importFrom(magick,image_info)
+importFrom(magick,image_join)
+importFrom(magick,image_modulate)
+importFrom(magick,image_negate)
+importFrom(magick,image_raster)
+importFrom(magick,image_read)
+importFrom(magick,image_resize)
+importFrom(magick,image_rotate)
+importFrom(magick,image_scale)
+importFrom(magick,image_write)
+importFrom(methods,"slot<-")
+importFrom(methods,as)
+importFrom(methods,is)
+importFrom(methods,new)
+importFrom(methods,slot)
+importFrom(methods,slotNames)
+importFrom(rjson,fromJSON)
+importFrom(rlang,"%||%")
+importFrom(rlang,'!!')
+importFrom(rlang,dots_list)
+importFrom(rlang,enquo)
+importFrom(rlang,eval_tidy)
+importFrom(rlang,list2)
+importFrom(rlang,quo_get_expr)
+importFrom(rlang,quo_name)
+importFrom(rlang,quo_text)
+importFrom(rlang,sym)
+importFrom(shiny,HTML)
+importFrom(shiny,reactiveValuesToList)
+importFrom(shiny,tags)
+importFrom(shiny,validateCssUnit)
+importFrom(shinyjs,hide)
+importFrom(shinyjs,show)
+importFrom(shinyjs,useShinyjs)
+importFrom(sp,point.in.polygon)
+importFrom(stats,aggregate)
+importFrom(stats,as.formula)
+importFrom(stats,dist)
+importFrom(stats,kmeans)
+importFrom(stats,loess)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,pnorm)
+importFrom(stats,predict)
+importFrom(stats,quantile)
+importFrom(stats,setNames)
+importFrom(stats,var)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_order)
+importFrom(stringr,str_remove)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_sort)
+importFrom(utils,.DollarNames)
+importFrom(utils,capture.output)
+importFrom(utils,head)
+importFrom(utils,read.csv)
+importFrom(utils,read.table)
+importFrom(uwot,umap)
+useDynLib(VoltRon)