# Generated by roxygen2: do not edit by hand

export(DE_between_group)
export(DE_between_time)
export(WGCNA_module)
export(calc_feature_property)
export(calc_mean_sd)
export(create_input)
export(decomp_variance)
export(enrichGO_list)
export(enrichGO_rank)
export(enrichR_list)
export(enrich_msigdb)
export(extract_hubs)
export(extract_segment_trends)
export(flatten_DE)
export(flatten_enrich)
export(get_custom_palette)
export(group_specific_features)
export(impute_groups)
export(merge_groups)
export(merge_replicates)
export(normalise_to_start)
export(plot_DE_between_group)
export(plot_DE_between_time)
export(plot_GO)
export(plot_ID)
export(plot_WGCNA)
export(plot_breakpoints)
export(plot_cor_matrix)
export(plot_cv)
export(plot_distribution)
export(plot_missing)
export(plot_modules_h)
export(plot_modules_v)
export(plot_pca)
export(plot_pca_3D)
export(plot_pca_arrows)
export(plot_pca_by_group)
export(plot_segments)
export(plot_trend)
export(plot_umap)
export(plot_umap_by_group)
export(plot_variance)
export(plot_volcano)
export(prepare_WGCNA)
export(prepare_tide)
export(run_Trendy)
export(run_WGCNA)
export(set_custom_palette)
export(split_groups)
export(summarise_Trendy)
export(summarise_feature_property)
export(summarise_module_metrics)
export(summarise_module_pattern)
export(theme_custom)
import(SummarizedExperiment)
import(ggplot2)
import(patchwork)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,anno_block)
importFrom(ComplexHeatmap,anno_link)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,anno_zoom)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,packLegend)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(PCAtools,getComponents)
importFrom(PCAtools,pairsplot)
importFrom(PCAtools,pca)
importFrom(PCAtools,plotloadings)
importFrom(PCAtools,screeplot)
importFrom(Trendy,breakpointDist)
importFrom(Trendy,formatResults)
importFrom(Trendy,plotFeature)
importFrom(Trendy,results)
importFrom(Trendy,topTrendy)
importFrom(Trendy,trendy)
importFrom(WGCNA,allowWGCNAThreads)
importFrom(WGCNA,binarizeCategoricalColumns)
importFrom(WGCNA,blockwiseModules)
importFrom(WGCNA,cor)
importFrom(WGCNA,corPvalueStudent)
importFrom(WGCNA,goodGenes)
importFrom(WGCNA,goodSamples)
importFrom(WGCNA,labeledHeatmap)
importFrom(WGCNA,labels2colors)
importFrom(WGCNA,moduleEigengenes)
importFrom(WGCNA,orderMEs)
importFrom(WGCNA,pickSoftThreshold)
importFrom(WGCNA,plotDendroAndColors)
importFrom(WGCNA,plotMEpairs)
importFrom(WGCNA,signedKME)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,bitr)
importFrom(clusterProfiler,cnetplot)
importFrom(clusterProfiler,dotplot)
importFrom(clusterProfiler,emapplot)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,gseGO)
importFrom(clusterProfiler,merge_result)
importFrom(clusterProfiler,simplify)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,anti_join)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,slice_head)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(enrichplot,pairwise_termsim)
importFrom(ggforce,geom_mark_ellipse)
importFrom(ggh4x,elem_list_rect)
importFrom(ggh4x,facet_grid2)
importFrom(ggh4x,strip_themed)
importFrom(ggplotify,as.ggplot)
importFrom(ggpubr,annotate_figure)
importFrom(ggpubr,ggarrange)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,text_grob)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggsci,pal_iterm)
importFrom(ggsci,pal_jco)
importFrom(ggsci,pal_simpsons)
importFrom(limma,contrasts.fit)
importFrom(limma,duplicateCorrelation)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(lme4,VarCorr)
importFrom(lme4,lmer)
importFrom(lme4,lmerControl)
importFrom(pbapply,pblapply)
importFrom(pbapply,pboptions)
importFrom(randtests,bartels.rank.test)
importFrom(scales,pal_hue)
importFrom(scales,pal_viridis)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,complete)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(umap,umap)
