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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(DE_multiomics)
export(GSEA)
export(OpenTarget_dataframe)
export(Transcription_Factor_enrichment)
export(Transcription_Factor_enrichment_supervised)
export(batch_correction_protein)
export(cell_type_enrichment)
export(circos_TF)
export(circular_corrplot)
export(clustering_DE_analysis)
export(combat_correction)
export(communities_network)
export(community_graph)
export(correlation_heatmap)
export(correlation_heatmap_clusters)
export(correlation_heatmap_supervised)
export(counts_rna)
export(enrichment_custom)
export(extract_loadings)
export(extract_multiomic_signature)
export(extract_weigths)
export(filter_protein)
export(format_res_deseq)
export(format_res_limma)
export(generate_multiassay)
export(getClustNum)
export(getStdiz)
export(get_background)
export(get_metadata)
export(integrate_with_DIABLO)
export(integrate_with_MBPLS)
export(integrate_with_MEFISTO)
export(integrate_with_MOFA)
export(integrate_with_iCluster)
export(integrate_with_sMBPLS)
export(integrated_enrichment_mutliGSEA)
export(integrative_results_clustering)
export(integrative_results_sparse_supervised)
export(integrative_results_supervised)
export(integrative_results_unsupervised)
export(interactive_network)
export(median_centering_correction)
export(multi_omic_report)
export(multi_omics_qc)
export(multiomics_heatmap)
export(multiomics_modules)
export(multiomics_network)
export(multiomics_network_matrix)
export(pathway_analysis_enrichr)
export(pathway_report)
export(plot_OpenTarget)
export(plot_communities)
export(plot_components)
export(plot_loadings)
export(plot_module_trajectory)
export(plot_optimal_cluster)
export(posterior_probability)
export(process_protein)
export(process_rna)
export(processed_proteomics)
export(processed_rna)
export(protein_DE_analysis)
export(proteomics_report)
export(pseudotime_inference)
export(qc_report)
export(rna_DE_analysis)
export(sign_signature)
export(single_omic_comparisons)
export(single_omic_report)
export(vertical_integration)
export(visualise_pathway)
export(volcano_interactive)
export(volcano_interactive_comparison)
export(volcano_plot_deseq)
export(volcano_plot_limma)
import(RColorBrewer)
import(SNFtool)
import(WGCNA)
import(circlize)
import(dplyr)
import(ggplot2)
import(igraph)
import(visNetwork)
importFrom(ActivePathways,read.GMT)
importFrom(AnnotationDbi,mapIds)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,results)
importFrom(EWCE,bootstrap_enrichment_test)
importFrom(EWCE,ewce_plot)
importFrom(EnsDb.Hsapiens.v86,EnsDb.Hsapiens.v86)
importFrom(GeneOverlap,drawHeatmap)
importFrom(GeneOverlap,newGOM)
importFrom(IntNMF,nmf.opt.k)
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,get_weights)
importFrom(MOFA2,plot_factors)
importFrom(MOFA2,plot_variance_explained)
importFrom(MOFA2,prepare_mofa)
importFrom(MOFA2,run_mofa)
importFrom(MOFA2,samples_metadata)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,assays)
importFrom(MultiAssayExperiment,colData)
importFrom(MultiAssayExperiment,complete.cases)
importFrom(MultiAssayExperiment,experiments)
importFrom(MultiAssayExperiment,getWithColData)
importFrom(MultiAssayExperiment,intersectRows)
importFrom(MultiAssayExperiment,listToMap)
importFrom(MultiAssayExperiment,metadata)
importFrom(MultiAssayExperiment,sampleMap)
importFrom(MultiAssayExperiment,wideFormat)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(WGCNA,GOenrichmentAnalysis)
importFrom(WGCNA,cor)
importFrom(WGCNA,moduleEigengenes)
importFrom(WGCNA,orderMEs)
importFrom(basetheme,num2col)
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(corrplot,corrplot)
importFrom(data.table,as.data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,top_n)
importFrom(dplyr,transmute)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(enrichR,enrichr)
importFrom(enrichplot,pairwise_termsim)
importFrom(fgsea,collapsePathways)
importFrom(fgsea,fgsea)
importFrom(ggplot2,alpha)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggpubr,ggscatter)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,rainbow)
importFrom(httr,POST)
importFrom(iClusterPlus,iClusterBayes)
importFrom(jsonlite,fromJSON)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,removeBatchEffect)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(magrittr,set_names)
importFrom(matrixStats,rowMins)
importFrom(mixOmics,block.pls)
importFrom(mixOmics,block.spls)
importFrom(mixOmics,block.splsda)
importFrom(mixOmics,selectVar)
importFrom(mixOmics,tune.block.splsda)
importFrom(mogsa,mbpca)
importFrom(mogsa,moGap)
importFrom(msigdbr,msigdbr)
importFrom(multiGSEA,combinePvalues)
importFrom(multiGSEA,extractPvalues)
importFrom(multiGSEA,getMultiOmicsFeatures)
importFrom(multiGSEA,initOmicsDataStructure)
importFrom(multiGSEA,multiGSEA)
importFrom(org.Hs.eg.db,org.Hs.eg.db)
importFrom(org.Mm.eg.db,org.Mm.eg.db)
importFrom(plotly,ggplotly)
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(psych,corr.test)
importFrom(purrr,discard)
importFrom(purrr,flatten)
importFrom(purrr,is_empty)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_dfr)
importFrom(purrr,possibly)
importFrom(reshape2,melt)
importFrom(slingshot,as.SlingshotDataSet)
importFrom(slingshot,slingshot)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,reorder)
importFrom(stringr,str_replace)
importFrom(stringr,str_wrap)
importFrom(tibble,enframe)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unnest)
importFrom(viridis,scale_color_viridis)
importFrom(visNetwork,toVisNetworkData)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visIgraphLayout)
importFrom(visNetwork,visLayout)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visNodes)