NAMESPACE

# Generated by roxygen2: do not edit by hand

export(add_cells)
export(add_counts)
export(add_embeddings)
export(build_vesalius_assay)
export(equalize_image)
export(filter_assay)
export(generate_embeddings)
export(generate_spix)
export(generate_tiles)
export(get_active_count_tag)
export(get_active_embedding_tag)
export(get_assay_names)
export(get_coordinates)
export(get_cost_contribution)
export(get_counts)
export(get_embeddings)
export(get_mapping_scores)
export(get_markers)
export(get_metric_clusters)
export(get_territories)
export(get_tiles)
export(identify_markers)
export(image_plot)
export(integrate_assays)
export(isolate_territories)
export(joint_territories)
export(layer_territory)
export(map_assays)
export(regularise_image)
export(search_log)
export(segment_image)
export(smooth_image)
export(summarise_territories)
export(territory_morphing)
export(territory_plot)
export(view_gene_expression)
export(view_mapping_metrics)
exportClasses(vesalius_assay)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,results)
importFrom(Matrix,Matrix)
importFrom(Matrix,rowMeans)
importFrom(NMF,coefficients)
importFrom(NMF,nmf)
importFrom(RANN,nn2)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rcpp,sourceCpp)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FetchData)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,IntegrateLayers)
importFrom(Seurat,Loadings)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Seurat,ScaleData)
importFrom(Seurat,VariableFeatures)
importFrom(SeuratObject,Features)
importFrom(Signac,FindTopFeatures)
importFrom(Signac,RunSVD)
importFrom(Signac,RunTFIDF)
importFrom(deldir,deldir)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,right_join)
importFrom(dplyr,select)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(future,nbrOfWorkers)
importFrom(future.apply,future_lapply)
importFrom(ggnewscale,new_scale)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_identity)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggpubr,ggarrange)
importFrom(grDevices,chull)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,gray)
importFrom(grDevices,rgb)
importFrom(igraph,cluster_leiden)
importFrom(igraph,cluster_louvain)
importFrom(igraph,distances)
importFrom(igraph,graph_from_data_frame)
importFrom(imager,add)
importFrom(imager,as.cimg)
importFrom(imager,average)
importFrom(imager,boxblur)
importFrom(imager,enorm)
importFrom(imager,grow)
importFrom(imager,imappend)
importFrom(imager,imgradient)
importFrom(imager,imrotate)
importFrom(imager,imsplit)
importFrom(imager,index.coord)
importFrom(imager,isoblur)
importFrom(imager,load.image)
importFrom(imager,map_il)
importFrom(imager,medianblur)
importFrom(imager,parmax)
importFrom(imager,parmin)
importFrom(imager,shrink)
importFrom(imager,spectrum)
importFrom(imager,split_connected)
importFrom(imager,threshold)
importFrom(imager,where)
importFrom(imagerExtra,BalanceSimplest)
importFrom(imagerExtra,EqualizeADP)
importFrom(imagerExtra,EqualizeDP)
importFrom(imagerExtra,EqualizePiecewise)
importFrom(imagerExtra,SPE)
importFrom(imagerExtra,ThresholdML)
importFrom(infix,"%||%")
importFrom(kohonen,som)
importFrom(kohonen,somgrid)
importFrom(lmtest,lrtest)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(patchwork,wrap_plots)
importFrom(purrr,map)
importFrom(purrr,map_dbl)
importFrom(sp,point.in.polygon)
importFrom(stats,IQR)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,chisq.test)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,ecdf)
importFrom(stats,fisher.test)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.exclude)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tools,toTitleCase)
importFrom(tvR,denoise2)
importFrom(utils,head)
importFrom(utils,tail)
useDynLib(vesalius)