NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export("%||%")
export(.send_enrichr_query)
export(Monocle2_diffex)
export(SetDefaultAssay)
export(add_census_slot)
export(add_percent_mito)
export(add_read_count_col)
export(allTranscripts)
export(allTranscriptsui)
export(annotate_cell_cycle)
export(annotate_excluded)
export(append_to_project_db)
export(arrange_ptime_heatmaps)
export(assign_clusters_to_cds)
export(build_bigwig_db)
export(by_row_corr_between_pt_heatmaps)
export(calc_cor_across_heatmaps)
export(calc_pseudotime_heatmap)
export(ccScore)
export(ccScoreui)
export(cells_selected)
export(changeEmbedParams)
export(changeEmbedParamsui)
export(clustering_workflow)
export(combine_cols)
export(combine_looms)
export(convert_human_seu_to_mouse)
export(convert_monoclev2_to_seuv3)
export(convert_mouse_seu_to_human)
export(convert_seu_list_to_multimodal)
export(convert_seu_to_cds)
export(convert_seurat_to_sce)
export(convert_seuv3_to_monoclev2)
export(convert_symbols_by_species)
export(convert_v3_to_v5)
export(create_proj_matrix)
export(create_project_db)
export(cross_check_heatmaps)
export(cross_species_integrate)
export(default_helper)
export(diffex)
export(diffexui)
export(dockerSeuratApp)
export(dropdownButton)
export(enframe_markers)
export(filter_low_rc_cells)
export(filter_merged_seu)
export(filter_merged_seus)
export(filter_rows_to_top)
export(findMarkers)
export(findMarkersui)
export(find_all_markers)
export(flip_pseudotime)
export(format_new_metadata)
export(format_pathway_table)
export(gene_test_plot)
export(genes_to_transcripts)
export(getEnrichedPathways)
export(get_meta)
export(get_transcripts_from_seu)
export(global_cellalign)
export(harmony_integrate)
export(integrateProj)
export(integrateProjui)
export(integration_workflow)
export(label_transfer)
export(learn_graph_by_resolution)
export(list_plot_types)
export(load_bigwigs)
export(load_counts_by_tximport)
export(load_meta)
export(load_seurat_from_proj)
export(load_seurat_path)
export(local_cellalign)
export(make_bigwig_db)
export(make_seuratTools_clean_names)
export(mem_str)
export(merge_loom)
export(merge_small_seus)
export(minimalSeuratApp)
export(monocle)
export(monocle_module_heatmap)
export(monocleui)
export(pad_sample_files)
export(pathwayEnrichment)
export(pathwayEnrichmentui)
export(plotClustree)
export(plotClustree_UI)
export(plotCoverage)
export(plotCoverage_UI)
export(plotDimRed)
export(plotDimRedui)
export(plotHeatmap)
export(plotHeatmapui)
export(plotReadCount)
export(plotReadCountui)
export(plotViolin)
export(plotViolinui)
export(plot_all_ptimes)
export(plot_all_transcripts)
export(plot_cds)
export(plot_cell_cycle_distribution)
export(plot_cells)
export(plot_feature)
export(plot_feature_in_ref_query_ptime)
export(plot_gene_coverage_by_var)
export(plot_markers)
export(plot_monocle_features)
export(plot_pseudotime)
export(plot_pseudotime_heatmap)
export(plot_readcount)
export(plot_scvelo)
export(plot_transcript_composition)
export(plot_var)
export(plot_violin)
export(prep_armor_meta)
export(prep_plot_genes_in_pseudotime)
export(prep_slider_values)
export(process_monocle_child)
export(propagate_spreadsheet_changes)
export(query_experiment)
export(read_project_db)
export(record_experiment_data)
export(reference_integrate)
export(reformatMetadataDR)
export(reformatMetadataDRui)
export(regress_by_features)
export(reintegrate_seu)
export(rename_seurat)
export(reorg_seurat_files)
export(reset_seu_meta)
export(run_BEAM)
export(run_census)
export(run_enrichmentbrowser)
export(run_hmap)
export(run_seurat_de)
export(save_seurat)
export(sce_from_tibbles)
export(scvelo_expression)
export(set_colnames_txi)
export(seu_calcn)
export(seu_complex_heatmap)
export(seu_from_tibbles)
export(seu_from_tximport)
export(seuratApp)
export(seuratToolsBox)
export(seurat_cluster)
export(seurat_find_markers)
export(seurat_integrate)
export(seurat_integration_pipeline)
export(seurat_preprocess)
export(seurat_process)
export(seurat_reduce_dimensions)
export(seurat_v5_integrate)
export(seurat_v5_integration_pipeline)
export(subset_by_meta)
export(swap_counts_from_feature)
export(tableSelected)
export(tableSelectedui)
export(techInfo)
export(techInfoui)
export(threshold_monocle_genes)
export(transcripts_to_genes)
export(unite_metadata)
export(update_exp_meta)
export(update_human_gene_symbols)
export(update_project_db)
export(update_seu_meta)
export(update_seuratTools_object)
export(velocyto_assay)
export(velocyto_seu)
export(velocyto_seurat_from_loom)
import(SingleCellExperiment)
import(dplyr)
importFrom(DataEditR,dataEditServer)
importFrom(DataEditR,dataEditUI)
importFrom(DataEditR,dataFilterServer)
importFrom(DataEditR,dataFilterUI)
importFrom(DataEditR,dataOutputServer)
importFrom(DataEditR,dataOutputUI)
importFrom(DataEditR,dataSelectServer)
importFrom(DataEditR,dataSelectUI)
importFrom(LoomExperiment,import)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,metadata)
importFrom(formattable,proportion)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(magrittr,"%>%")
importFrom(purrr,"%||%")
importFrom(rlang,"%||%")
importFrom(rlang,.data)
importFrom(scater,plotDots)
importFrom(scater,plotExpression)
importFrom(scater,plotPCA)
importFrom(scater,plotReducedDim)
importFrom(scater,runPCA)
importFrom(scater,runTSNE)
importFrom(scater,runUMAP)
importFrom(scran,buildSNNGraph)
importFrom(scran,clusterCells)
importFrom(scran,computeSumFactors)
importFrom(scran,cyclone)
importFrom(scran,findMarkers)
importFrom(scran,getClusteredPCs)
importFrom(scran,getTopHVGs)
importFrom(scran,modelGeneVar)
importFrom(scran,quickCluster)
importFrom(scuttle,addPerCellQCMetrics)
importFrom(scuttle,logNormCounts)
importFrom(shinyjs,alert)
importFrom(shinyjs,hidden)
importFrom(shinyjs,html)
importFrom(shinyjs,runcodeServer)
importFrom(shinyjs,runcodeUI)
importFrom(shinyjs,useShinyjs)
importFrom(velociraptor,embedVelocity)
importFrom(velociraptor,gridVectors)
importFrom(velociraptor,scvelo)