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NAMESPACE
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175 lines (174 loc) · 5.06 KB
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# Generated by roxygen2: do not edit by hand
export("analysis_type<-")
export("directed_scores<-")
export("hotspots<-")
export("influence_map<-")
export("interactions<-")
export("lr_scores<-")
export("overlap_scores<-")
export("spatial_params<-")
export("spatial_patterns<-")
export("undirected_scores<-")
export(SpaceMarkers)
export(SpaceMarkersExperiment)
export(add_features)
export(analysis_type)
export(assay)
export(assays)
export(calculate_gene_scores_directed)
export(calculate_gene_set_score)
export(calculate_gene_set_specificity)
export(calculate_influence)
export(calculate_lr_scores)
export(calculate_overlap_directed)
export(calculate_overlap_undirected)
export(calculate_thresholds)
export(colData)
export(create_lr_dataframe)
export(directed_scores)
export(find_all_hotspots)
export(find_hotspots_gmm)
export(find_pattern_hotspots)
export(get_im_scores)
export(get_interacting_genes)
export(get_pairwise_interacting_genes)
export(get_spatial_features)
export(get_spatial_parameters)
export(get_spatial_params_morans_i)
export(hotspots)
export(imgRaster)
export(influence_map)
export(interactions)
export(load10X)
export(load10XCoords)
export(load10XExpr)
export(load_anndata)
export(lr_scores)
export(overlap_map)
export(overlap_scores)
export(params)
export(plot_cell_interaction_circos)
export(plot_im_scores)
export(plot_overlap_scores)
export(plot_source_to_target_circos)
export(plot_spatial)
export(plot_spatial_data_over_image)
export(plot_target_from_sources_circos)
export(rowData)
export(save_anndata)
export(spatialCoords)
export(spatial_params)
export(spatial_patterns)
export(undirected_scores)
exportClasses(SpaceMarkersExperiment)
exportMethods("analysis_type<-")
exportMethods("directed_scores<-")
exportMethods("hotspots<-")
exportMethods("influence_map<-")
exportMethods("interactions<-")
exportMethods("lr_scores<-")
exportMethods("overlap_scores<-")
exportMethods("spatial_params<-")
exportMethods("spatial_patterns<-")
exportMethods("undirected_scores<-")
exportMethods(analysis_type)
exportMethods(calculate_gene_scores_directed)
exportMethods(calculate_gene_set_score)
exportMethods(calculate_gene_set_specificity)
exportMethods(calculate_influence)
exportMethods(calculate_lr_scores)
exportMethods(calculate_overlap_directed)
exportMethods(calculate_overlap_undirected)
exportMethods(directed_scores)
exportMethods(find_all_hotspots)
exportMethods(find_hotspots_gmm)
exportMethods(get_im_scores)
exportMethods(get_pairwise_interacting_genes)
exportMethods(hotspots)
exportMethods(influence_map)
exportMethods(interactions)
exportMethods(lr_scores)
exportMethods(overlap_scores)
exportMethods(params)
exportMethods(spatial_params)
exportMethods(spatial_patterns)
exportMethods(undirected_scores)
import(RColorBrewer)
import(circlize)
import(ggplot2)
importClassesFrom(SpatialExperiment,SpatialExperiment)
importFrom(Matrix,sparseMatrix)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SpatialExperiment,"spatialCoords<-")
importFrom(SpatialExperiment,SpatialExperiment)
importFrom(SpatialExperiment,imgRaster)
importFrom(SpatialExperiment,spatialCoords)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(ape,Moran.I)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(effsize,cohen.d)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_raster)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(hdf5r,h5file)
importFrom(jsonlite,read_json)
importFrom(matrixStats,count)
importFrom(matrixTests,row_kruskalwallis)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(mixtools,normalmixEM)
importFrom(nanoparquet,read_parquet)
importFrom(qvalue,qvalue)
importFrom(readbitmap,read.bitmap)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(rstatix,filter)
importFrom(spatstat.explore,Smooth)
importFrom(spatstat.geom,marks)
importFrom(spatstat.geom,owin)
importFrom(spatstat.geom,ppp)
importFrom(stats,complete.cases)
importFrom(stats,dist)
importFrom(stats,lag)
importFrom(stats,na.omit)
importFrom(stats,pnorm)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(viridis,scale_fill_viridis)