# Generated by roxygen2: do not edit by hand

export(association_models)
export(build_ont_annot_app)
export(compare_association)
export(create_exposomicset)
export(download_dataset)
export(extract_omics_exposure_df)
export(extract_results)
export(extract_results_excel)
export(extract_top_factor_features)
export(filter_missing)
export(filter_non_normal)
export(filter_omics)
export(filter_sample_outliers)
export(load_annotation_data)
export(make_example_data)
export(make_example_sc)
export(make_example_sce_codebook)
export(pivot_exp)
export(pivot_feature)
export(pivot_sample)
export(plot_association)
export(plot_association_comparison)
export(plot_circos_correlation)
export(plot_clusters)
export(plot_correlation_summary)
export(plot_correlation_tile)
export(plot_enrichment)
export(plot_exposure_impact)
export(plot_exposure_omics_association)
export(plot_exposures)
export(plot_factor_summary)
export(plot_manhattan)
export(plot_missing)
export(plot_network)
export(plot_normality_summary)
export(plot_pca)
export(plot_sample_clusters)
export(plot_sensitivity_summary)
export(plot_top_factor_features)
export(plot_volcano)
export(run_association)
export(run_cluster_exposures)
export(run_cluster_samples)
export(run_correlation)
export(run_create_network)
export(run_differential_abundance)
export(run_enrichment)
export(run_exposome_score)
export(run_exposure_impact)
export(run_exposure_omics_association)
export(run_factor_overlap)
export(run_impute_missing)
export(run_multiomics_integration)
export(run_normality_check)
export(run_pca)
export(run_pipeline_summary)
export(run_sensitivity_analysis)
export(run_summarize_exposures)
export(transform_exposure)
export(transform_sce_to_exposomicset)
import(fenr)
import(ggplot2)
importFrom(BiocFileCache,
  BiocFileCache,
  bfcrpath
)
importFrom(DT,
  DTOutput,
  dataTableProxy,
  datatable,
  formatStyle,
  renderDT,
  replaceData,
  styleEqual
)
importFrom(Hmisc,rcorr)
importFrom(MASS,boxcox)
importFrom(Matrix,
  rowSums,
  sparseMatrix,
  tcrossprod
)
importFrom(MultiAssayExperiment,
  colData,
  experiments,
  metadata
)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,
  assay,
  assays,
  colData,
  rowData
)
importFrom(broom,tidy)
importFrom(cluster,
  clusGap,
  daisy,
  diana,
  maxSE
)
importFrom(dplyr,
  across,
  add_count,
  all_of,
  any_of,
  arrange,
  bind_cols,
  bind_rows,
  case_when,
  count,
  desc,
  distinct,
  everything,
  filter,
  full_join,
  group_by,
  if_else,
  inner_join,
  left_join,
  matches,
  mutate,
  mutate_all,
  mutate_if,
  n,
  percent_rank,
  pull,
  reframe,
  rename,
  row_number,
  select,
  select_if,
  semi_join,
  slice_head,
  summarise,
  sym,
  top_n,
  ungroup,
  where
)
importFrom(factoextra,
  fviz_eig,
  fviz_nbclust,
  hcut
)
importFrom(ggplot2,
  aes,
  coord_flip,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_grid,
  facet_wrap,
  geom_bar,
  geom_boxplot,
  geom_col,
  geom_hline,
  geom_jitter,
  geom_point,
  geom_segment,
  geom_tile,
  geom_vline,
  ggplot,
  guide_legend,
  guides,
  labs,
  margin,
  scale_color_gradient,
  scale_color_identity,
  scale_color_manual,
  scale_fill_gradient,
  scale_fill_gradient2,
  scale_fill_manual,
  scale_size_continuous,
  scale_x_log10,
  scale_y_continuous,
  scale_y_log10,
  theme,
  theme_bw,
  theme_minimal,
  theme_void
)
importFrom(ggpubr,
  get_palette,
  rotate_x_text,
  theme_pubclean,
  theme_pubr
)
importFrom(ggrepel,
  geom_label_repel,
  geom_text_repel
)
importFrom(httr,
  GET,
  status_code,
  timeout
)
importFrom(igraph,
  cluster_louvain,
  gorder,
  graph_from_data_frame
)
importFrom(jsonlite,fromJSON)
importFrom(limma,
  contrasts.fit,
  eBayes,
  lmFit,
  makeContrasts,
  topTable
)
importFrom(methods,as)
importFrom(naniar,
  impute_mean_all,
  impute_median_all,
  miss_var_summary
)
importFrom(purrr,
  compact,
  discard,
  imap,
  iwalk,
  map,
  map2,
  pluck,
  reduce
)
importFrom(readr,parse_number)
importFrom(rlang,
  "%||%",
  .data,
  sym
)
importFrom(scales,alpha)
importFrom(shiny,
  HTML,
  actionButton,
  addResourcePath,
  column,
  div,
  downloadButton,
  fileInput,
  fluidPage,
  fluidRow,
  h4,
  hr,
  img,
  modalDialog,
  numericInput,
  observeEvent,
  reactiveValues,
  renderUI,
  req,
  selectInput,
  selectizeInput,
  shinyApp,
  showModal,
  tags,
  titlePanel,
  uiOutput,
  updateSelectizeInput
)
importFrom(stats,
  IQR,
  as.dist,
  as.formula,
  binomial,
  coef,
  cor,
  cov,
  cutree,
  dist,
  end,
  family,
  glm,
  hclust,
  logLik,
  median,
  model.matrix,
  na.omit,
  p.adjust,
  prcomp,
  qchisq,
  qt,
  quantile,
  reorder,
  rlnorm,
  rnorm,
  runif,
  sd,
  setNames,
  shapiro.test,
  start,
  var
)
importFrom(stringr,
  str_extract,
  str_remove,
  str_replace_all,
  str_trim
)
importFrom(tibble,
  as_tibble,
  column_to_rownames,
  enframe,
  rownames_to_column,
  tibble
)
importFrom(tidyr,
  pivot_longer,
  separate_rows
)
importFrom(tools,md5sum)
importFrom(utils,
  URLencode,
  data,
  head,
  modifyList,
  tail
)
importMethodsFrom(tidybulk,identify_abundant)
importMethodsFrom(tidybulk,pivot_sample)
importMethodsFrom(tidybulk,pivot_transcript)
importMethodsFrom(tidybulk,test_differential_abundance)
