# 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_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_c)
export(vis_clus_p)
export(vis_gene)
export(vis_gene_c)
export(vis_gene_p)
export(vis_grid_clus)
export(vis_grid_gene)
export(vis_image)
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,
  anno_barplot,
  columnAnnotation,
  rowAnnotation
)
importFrom(DT,
  DTOutput,
  renderDT
)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,
  CharacterList,
  IntegerList
)
importFrom(S4Vectors,
  "mcols<-",
  DataFrame,
  mcols,
  metadata
)
importFrom(SingleCellExperiment,logcounts)
importFrom(SpatialExperiment,
  "colData<-",
  "imgData<-",
  "spatialCoords<-",
  "spatialCoordsNames<-",
  SpatialImage,
  addImg,
  imgData,
  imgRaster,
  read10xVisium,
  scaleFactors,
  spatialCoords
)
importFrom(SummarizedExperiment,
  "colData<-",
  "rowData<-",
  "rowRanges<-",
  assay,
  assayNames,
  assays,
  colData
)
importFrom(benchmarkme,get_ram)
importFrom(circlize,colorRamp2)
importFrom(cowplot,plot_grid)
importFrom(dplyr,
  group_by,
  left_join,
  mutate,
  select,
  summarize
)
importFrom(edgeR,
  calcNormFactors,
  filterByExpr
)
importFrom(golem,with_golem_options)
importFrom(grDevices,
  as.raster,
  dev.off,
  pdf
)
importFrom(graphics,
  boxplot,
  par,
  points
)
importFrom(grid,
  rasterGrob,
  unit
)
importFrom(jsonlite,read_json)
importFrom(limma,
  contrasts.fit,
  duplicateCorrelation,
  eBayes,
  lmFit,
  makeContrasts,
  topTable
)
importFrom(magick,
  image_background,
  image_channel,
  image_contrast,
  image_enhance,
  image_equalize,
  image_median,
  image_modulate,
  image_negate,
  image_quantize,
  image_read,
  image_transparent
)
importFrom(methods,
  is,
  new
)
importFrom(png,readPNG)
importFrom(rlang,arg_match)
importFrom(rtracklayer,import)
importFrom(scater,plotReducedDim)
importFrom(scrapper,aggregateAcrossCells)
importFrom(scuttle,isOutlier)
importFrom(sessioninfo,session_info)
importFrom(shiny,shinyApp)
importFrom(shinyWidgets,
  pickerInput,
  pickerOptions,
  updatePickerInput
)
importFrom(statmod,mixedModel2Fit)
importFrom(stats,
  cor,
  dist,
  fisher.test,
  hclust,
  median,
  model.matrix,
  p.adjust,
  prcomp,
  reshape,
  setNames
)
importFrom(tibble,tibble)
importFrom(utils,
  combn,
  read.csv,
  write.csv
)
importFrom(viridisLite,viridis)
importMethodsFrom(Matrix,colSums)
