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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(add_empirical_pval_fdr)
export(add_extra_criterion)
export(alias_to_symbol_SCE)
export(combine_sender_receiver_de)
export(combine_sender_receiver_info_ic)
export(compare_normal_emp_pvals)
export(fix_frq_df)
export(generate_prioritization_tables)
export(generate_prioritization_tables_condition_specific_celltypes_receiver)
export(generate_prioritization_tables_condition_specific_celltypes_sender)
export(generate_prioritization_tables_sampleAgnostic_multifactorial)
export(get_DE_info)
export(get_DE_info_sampleAgnostic)
export(get_FDR_empirical)
export(get_FDR_empirical_plots)
export(get_FDR_empirical_plots_all)
export(get_abundance_info)
export(get_avg_pb_exprs)
export(get_empirical_pvals)
export(get_frac_exprs)
export(get_frac_exprs_sampleAgnostic)
export(get_ligand_activities_targets_DEgenes)
export(get_ligand_activities_targets_DEgenes_beta)
export(get_muscat_exprs_avg)
export(get_muscat_exprs_frac)
export(get_pseudobulk_logCPM_exprs)
export(get_top_n_lr_pairs)
export(infer_intercellular_regulatory_network)
export(lr_target_prior_cor_inference)
export(make_DEgene_dotplot_pseudobulk)
export(make_DEgene_dotplot_pseudobulk_batch)
export(make_DEgene_dotplot_pseudobulk_reversed)
export(make_circos_group_comparison)
export(make_circos_one_group)
export(make_ggraph_ligand_target_links)
export(make_ggraph_signaling_path)
export(make_ligand_activity_plots)
export(make_ligand_activity_target_plot)
export(make_ligand_receptor_violin_plot)
export(make_lite_output)
export(make_lite_output_condition_specific)
export(make_lr_target_correlation_plot)
export(make_lr_target_prior_cor_heatmap)
export(make_lr_target_scatter_plot)
export(make_sample_lr_prod_activity_batch_plots)
export(make_sample_lr_prod_activity_plots)
export(make_sample_lr_prod_activity_plots_Omnipath)
export(make_sample_lr_prod_plots)
export(make_target_violin_plot)
export(makenames_SCE)
export(multi_nichenet_analysis)
export(multi_nichenet_analysis_sampleAgnostic)
export(p.adjust_empirical)
export(perform_muscat_de_analysis)
export(prioritize_condition_specific_receiver)
export(prioritize_condition_specific_sender)
export(process_abund_info)
export(process_abundance_expression_info)
export(process_geneset_data)
export(process_info_to_ic)
export(visualize_network)
import(circlize)
import(doParallel)
import(dplyr)
import(foreach)
import(ggplot2)
import(ggraph)
import(locfdr)
import(muscat)
import(nichenetr)
import(tibble)
import(tidyr)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,draw)
importFrom(Hmisc,rcorr)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,logcounts)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(UpSetR,upset)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(generics,intersect)
importFrom(generics,setdiff)
importFrom(generics,union)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggpubr,as_ggplot)
importFrom(grDevices,recordPlot)
importFrom(graphics,hist)
importFrom(graphics,lines)
importFrom(igraph,graph_from_data_frame)
importFrom(limma,makeContrasts)
importFrom(magrittr,set_names)
importFrom(magrittr,set_rownames)
importFrom(muscat,prepSCE)
importFrom(nichenetr,make_heatmap_ggplot)
importFrom(nichenetr,prepare_ligand_target_visualization)
importFrom(nichenetr,scale_quantile)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(patchwork,wrap_plots)
importFrom(purrr,map)
importFrom(scater,computeLibraryFactors)
importFrom(scater,logNormCounts)
importFrom(scran,findMarkers)
importFrom(stats,dnorm)
importFrom(stats,glm)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,poly)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stringr,str_split)
importFrom(sva,ComBat_seq)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidygraph,as_tbl_graph)
importFrom(tidyr,expand)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(viridis,scale_color_viridis)