# Generated by roxygen2: do not edit by hand

export(DE_between_group)
export(DE_between_time)
export(DE_timecourse)
export(WGCNA_module)
export(calc_feature_property)
export(calc_mean_sd)
export(combine_tide)
export(create_input)
export(decomp_variance)
export(enrichGO_list)
export(enrichGO_rank)
export(enrichR_list)
export(enrich_msigdb)
export(extract_consensus_hubs)
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_scatter)
export(plot_segments)
export(plot_trend)
export(plot_umap)
export(plot_umap_by_group)
export(plot_upset_h)
export(plot_upset_v)
export(plot_variance)
export(plot_volcano)
export(prepare_WGCNA)
export(prepare_tide)
export(run_Trendy)
export(run_WGCNA)
export(run_consensus_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,
  HeatmapAnnotation,
  Legend,
  anno_block,
  anno_link,
  anno_mark,
  anno_zoom,
  draw,
  packLegend,
  rowAnnotation
)
importFrom(PCAtools,
  getComponents,
  pairsplot,
  pca,
  plotloadings,
  screeplot
)
importFrom(Trendy,
  breakpointDist,
  formatResults,
  plotFeature,
  results,
  topTrendy,
  trendy
)
importFrom(WGCNA,
  allowWGCNAThreads,
  binarizeCategoricalColumns,
  blockwiseModules,
  cor,
  corPvalueStudent,
  goodGenes,
  goodSamples,
  labeledHeatmap,
  labels2colors,
  moduleEigengenes,
  orderMEs,
  pickSoftThreshold,
  plotDendroAndColors,
  plotMEpairs,
  signedKME
)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,
  bitr,
  cnetplot,
  dotplot,
  emapplot,
  enrichGO,
  gseGO,
  merge_result,
  simplify
)
importFrom(dplyr,
  across,
  all_of,
  anti_join,
  arrange,
  bind_rows,
  count,
  desc,
  distinct,
  everything,
  filter,
  full_join,
  group_by,
  mutate,
  n,
  n_distinct,
  pull,
  rename,
  row_number,
  select,
  slice,
  slice_head,
  slice_min,
  summarise,
  ungroup
)
importFrom(enrichplot,pairwise_termsim)
importFrom(ggforce,geom_mark_ellipse)
importFrom(ggh4x,
  elem_list_rect,
  facet_grid2,
  facet_wrap2,
  strip_nested,
  strip_themed
)
importFrom(ggplotify,as.ggplot)
importFrom(ggpubr,
  annotate_figure,
  ggarrange,
  stat_compare_means,
  text_grob
)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggsci,
  pal_iterm,
  pal_jco,
  pal_simpsons
)
importFrom(limma,
  contrasts.fit,
  duplicateCorrelation,
  eBayes,
  lmFit,
  makeContrasts,
  topTable
)
importFrom(lme4,
  VarCorr,
  lmer,
  lmerControl
)
importFrom(pbapply,
  pblapply,
  pboptions
)
importFrom(randtests,bartels.rank.test)
importFrom(scales,
  pal_hue,
  pal_viridis
)
importFrom(tibble,
  column_to_rownames,
  rownames_to_column
)
importFrom(tidyr,
  complete,
  pivot_longer,
  pivot_wider,
  unite
)
importFrom(umap,umap)
