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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(add10xVisiumAnalysis)
export(add_images)
export(add_key)
export(add_qc_metrics)
export(annotate_registered_clusters)
export(check_modeling_results)
export(check_sce)
export(check_sce_layer)
export(check_spe)
export(cluster_export)
export(cluster_import)
export(enough_ram)
export(fetch_data)
export(frame_limits)
export(gene_set_enrichment)
export(gene_set_enrichment_plot)
export(geom_spatial)
export(get_colors)
export(img_edit)
export(img_update)
export(img_update_all)
export(layer_boxplot)
export(layer_matrix_plot)
export(layer_stat_cor)
export(layer_stat_cor_plot)
export(locate_images)
export(read10xVisiumAnalysis)
export(read10xVisiumWrapper)
export(registration_block_cor)
export(registration_model)
export(registration_pseudobulk)
export(registration_stats_anova)
export(registration_stats_enrichment)
export(registration_stats_pairwise)
export(registration_wrapper)
export(run_app)
export(sce_to_spe)
export(sig_genes_extract)
export(sig_genes_extract_all)
export(sort_clusters)
export(vis_clus)
export(vis_clus_p)
export(vis_gene)
export(vis_gene_p)
export(vis_grid_clus)
export(vis_grid_gene)
import(ExperimentHub)
import(MatrixGenerics)
import(SingleCellExperiment)
import(ggplot2)
import(grid)
import(paletteer)
import(plotly, except = last_plot)
import(shiny)
importFrom(AnnotationHub,query)
importFrom(BiocGenerics,which)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DT,DTOutput)
importFrom(DT,renderDT)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IntegerList)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,logcounts)
importFrom(SpatialExperiment,"colData<-")
importFrom(SpatialExperiment,"imgData<-")
importFrom(SpatialExperiment,"spatialCoords<-")
importFrom(SpatialExperiment,"spatialCoordsNames<-")
importFrom(SpatialExperiment,SpatialImage)
importFrom(SpatialExperiment,addImg)
importFrom(SpatialExperiment,imgData)
importFrom(SpatialExperiment,imgRaster)
importFrom(SpatialExperiment,read10xVisium)
importFrom(SpatialExperiment,scaleFactors)
importFrom(SpatialExperiment,spatialCoords)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(benchmarkme,get_ram)
importFrom(circlize,colorRamp2)
importFrom(cowplot,plot_grid)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,filterByExpr)
importFrom(fields,image.plot)
importFrom(golem,with_golem_options)
importFrom(grDevices,as.raster)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,boxplot)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(grid,rasterGrob)
importFrom(grid,unit)
importFrom(jsonlite,read_json)
importFrom(limma,contrasts.fit)
importFrom(limma,duplicateCorrelation)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(magick,image_background)
importFrom(magick,image_channel)
importFrom(magick,image_contrast)
importFrom(magick,image_enhance)
importFrom(magick,image_equalize)
importFrom(magick,image_median)
importFrom(magick,image_modulate)
importFrom(magick,image_negate)
importFrom(magick,image_quantize)
importFrom(magick,image_read)
importFrom(magick,image_transparent)
importFrom(methods,is)
importFrom(methods,new)
importFrom(png,readPNG)
importFrom(rlang,arg_match)
importFrom(rtracklayer,import)
importFrom(scater,plotReducedDim)
importFrom(scuttle,aggregateAcrossCells)
importFrom(scuttle,isOutlier)
importFrom(sessioninfo,session_info)
importFrom(shiny,shinyApp)
importFrom(shinyWidgets,pickerInput)
importFrom(shinyWidgets,pickerOptions)
importFrom(shinyWidgets,updatePickerInput)
importFrom(statmod,mixedModel2Fit)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,reshape)
importFrom(stats,setNames)
importFrom(tibble,tibble)
importFrom(utils,combn)
importFrom(utils,read.csv)
importFrom(utils,write.csv)
importFrom(viridisLite,viridis)
importMethodsFrom(Matrix,colSums)