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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(.communities_network)
export(.community_graph)
export(.dot_plot_enrichr_semantics)
export(.get_ID_names)
export(.get_ID_type)
export(.get_background)
export(.get_metadata)
export(.get_multimodal_object)
export(.impute_distribution)
export(.impute_minimum_value)
export(.interactive_network)
export(.multiomics_network)
export(.multiomics_network_cluster)
export(.multiomics_network_matrix)
export(DE_multiomics)
export(GSEA)
export(MOFA_get_relevant_factor)
export(OpenTargets)
export(batch_correction_protein)
export(cell_type_enrichment)
export(circular_corrplot)
export(combat_correction)
export(counts_rna)
export(enrichment_custom)
export(extract_multiomic_signature)
export(extract_weigths)
export(filter_protein)
export(format_res_deseq)
export(format_res_limma)
export(generate_multiassay)
export(get_module_annotation)
export(integrate_with_DIABLO)
export(integrate_with_MBPLS)
export(integrate_with_MEIFESTO)
export(integrate_with_MOFA)
export(integrate_with_sMBPLS)
export(integrative_results_clustering)
export(integrative_results_supervised)
export(integrative_results_unsupervised)
export(median_centering_correction)
export(multiomics_modules)
export(pathway_analysis_enrichr)
export(process_protein)
export(process_rna)
export(processed_proteomics)
export(processed_rna)
export(protein_DE_analysis)
export(pseudotime_inference)
export(pseudotime_ordering_modules)
export(rna_DE_analysis)
export(single_omic_comparisons)
export(vertical_integration)
export(volcano_interactive)
export(volcano_interactive_comparison)
export(volcano_plot_deseq)
export(volcano_plot_limma)
import(MOFA2)
import(MultiAssayExperiment)
import(basilisk)
import(dplyr)
import(fgsea)
import(ggplot2)
import(ggrepel)
import(lme4)
import(mixOmics)
import(plotly)
import(reticulate)
importFrom(AnnotationDbi,select)
importFrom(ClassDiscovery,distanceMatrix)
importFrom(ComplexHeatmap,"%v%")
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,ht_opt)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,results)
importFrom(MOFA2,correlate_factors_with_covariates)
importFrom(MOFA2,create_mofa)
importFrom(MOFA2,get_default_data_options)
importFrom(MOFA2,get_default_mefisto_options)
importFrom(MOFA2,get_default_model_options)
importFrom(MOFA2,get_default_training_options)
importFrom(MOFA2,plot_factors)
importFrom(MOFA2,prepare_mofa)
importFrom(MOFA2,run_mofa)
importFrom(MOFA2,samples_metadata)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,colData)
importFrom(MultiAssayExperiment,getWithColData)
importFrom(MultiAssayExperiment,listToMap)
importFrom(MultiAssayExperiment,sampleMap)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(WGCNA,cor)
importFrom(WGCNA,moduleEigengenes)
importFrom(WGCNA,orderMEs)
importFrom(assertthat,assert_that)
importFrom(circlize,colorRamp2)
importFrom(cli,cli_alert_danger)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_text)
importFrom(cli,style_bold)
importFrom(clusterProfiler,compareCluster)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,simplify)
importFrom(corrplot,corrplot)
importFrom(cowplot,background_grid)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,mutate)
importFrom(enrichR,enrichr)
importFrom(enrichR,listEnrichrDbs)
importFrom(enrichplot,pairwise_termsim)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggpubr,ggscatter)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,removeBatchEffect)
importFrom(limma,topTable)
importFrom(magrittr,set_names)
importFrom(matrixStats,rowMins)
importFrom(mixOmics,block.pls)
importFrom(mixOmics,block.spls)
importFrom(mixOmics,block.splsda)
importFrom(mixOmics,tune.block.splsda)
importFrom(msigdbr,msigdbr)
importFrom(proBatch,center_feature_batch_medians_df)
importFrom(proBatch,correct_with_ComBat_df)
importFrom(proBatch,long_to_matrix)
importFrom(proBatch,matrix_to_long)
importFrom(proBatch,quantile_normalize_dm)
importFrom(purrr,discard)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_dfr)
importFrom(purrr,possibly)
importFrom(slingshot,as.SlingshotDataSet)
importFrom(slingshot,slingshot)
importFrom(stats,as.formula)
importFrom(stats,model.matrix)
importFrom(stats,prcomp)
importFrom(stats,reorder)
importFrom(stringr,str_wrap)
importFrom(tibble,enframe)
importFrom(viridis,scale_color_viridis)