# Generated by roxygen2: do not edit by hand

export(MG_shapes)
export(Pre_processing_hashcodes)
export(Pre_processing_species)
export(Pre_processing_species_list)
export(RandomForest_selected)
export(adjust_abundance_by_factor)
export(adjust_abundance_one_third)
export(adjusted_prevalence)
export(alluvial_plot)
export(calculate_list_average_scaling_factors)
export(calculate_spikeIn_factors)
export(calculate_spike_percentage)
export(calculate_spike_percentage_list)
export(calculate_summary_stats_table)
export(color_palette)
export(conclusion)
export(convert_categorical_to_factors)
export(convert_phyloseq_to_tse)
export(convert_to_absolute_counts)
export(convert_tse_to_phyloseq)
export(create_directory)
export(degree_network)
export(detect_common_asvs_taxa)
export(extract_neighbors)
export(filter_and_split_abundance)
export(get_long_format_data)
export(get_otu_table)
export(get_phy_tree)
export(get_reference_seq)
export(get_sample_data)
export(get_sample_sums)
export(get_tax_table)
export(gm_mean)
export(imbalance_calculate_list_average_scaling_factors)
export(label)
export(load_graphml)
export(my_custom_theme)
export(node_level_metrics)
export(norm.DESeq)
export(normalization_set)
export(perform_and_visualize_DA)
export(plot_core_microbiome_custom)
export(plot_spikein_tree_diagnostic)
export(plotbar_abundance)
export(proportion_adj)
export(quadrant_plot)
export(random_subsample_WithReductionFactor)
export(randomsubsample_Trimmed_evenDepth)
export(regression_plot)
export(relativized_filtered_taxa)
export(remove_zero_negative_count_samples)
export(ridge_plot_it)
export(set_nf)
export(simulate_network_robustness)
export(summ_ASV_OTUID)
export(summ_count_phyloseq)
export(summ_phyloseq_sampleID)
export(taxa_barplot)
export(tidy_phyloseq_tse)
export(validate_spikein_clade)
export(weight_Network)
exportClasses(ExpData)
importFrom(Biostrings,
  DNAStringSet,
  readDNAStringSet
)
importFrom(DECIPHER,AlignSeqs)
importFrom(DESeq2,
  "dispersions<-",
  DESeq,
  DESeqDataSetFromMatrix,
  counts,
  estimateDispersionsGeneEst,
  estimateSizeFactors,
  estimateSizeFactorsForMatrix,
  nbinomWaldTest,
  results,
  sizeFactors
)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,
  DataFrame,
  metadata
)
importFrom(SummarizedExperiment,
  "assay<-",
  "rowData<-",
  SummarizedExperiment,
  assay,
  assays,
  colData,
  colnames,
  mcols,
  rowData
)
importFrom(TreeSummarizedExperiment,
  "referenceSeq<-",
  TreeSummarizedExperiment,
  referenceSeq,
  rowTree
)
importFrom(ape,
  as.phylo,
  boot.phylo,
  cophenetic.phylo,
  drop.tip,
  edgelabels,
  getMRCA,
  is.monophyletic,
  is.rooted,
  ladderize,
  nj,
  nodelabels,
  plot.phylo,
  prop.clades,
  root,
  tiplabels,
  write.tree
)
importFrom(data.table,":=")
importFrom(dplyr,
  across,
  all_of,
  arrange,
  bind_cols,
  case_when,
  desc,
  distinct,
  filter,
  group_by,
  if_else,
  left_join,
  mutate,
  mutate_at,
  pull,
  rename,
  rename_with,
  select,
  select_if,
  slice_head,
  summarise,
  summarise_all,
  summarize,
  top_n,
  ungroup,
  where
)
importFrom(edgeR,
  DGEList,
  calcNormFactors,
  estimateDisp,
  glmFit,
  glmLRT,
  topTags
)
importFrom(flextable,
  align,
  autofit,
  bg,
  bold,
  color,
  flextable,
  font,
  fontsize,
  italic,
  save_as_docx,
  set_caption,
  theme_vanilla,
  width
)
importFrom(ggalluvial,
  geom_alluvium,
  geom_stratum,
  is_alluvia_form
)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,
  aes,
  aes_string,
  after_stat,
  coord_flip,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_grid,
  facet_wrap,
  geom_bar,
  geom_boxplot,
  geom_histogram,
  geom_hline,
  geom_label,
  geom_line,
  geom_linerange,
  geom_point,
  geom_smooth,
  geom_text,
  geom_tile,
  geom_vline,
  ggplot,
  ggsave,
  ggtitle,
  guide_legend,
  guides,
  labs,
  position_dodge,
  scale_alpha_continuous,
  scale_color_manual,
  scale_color_viridis_c,
  scale_fill_gradient,
  scale_fill_manual,
  scale_fill_viridis_d,
  scale_size_continuous,
  scale_x_discrete,
  scale_y_continuous,
  theme,
  theme_bw,
  theme_minimal,
  theme_void,
  unit,
  xlab,
  ylab
)
importFrom(ggpubr,
  color_palette,
  stat_cor,
  stat_regline_equation
)
importFrom(ggraph,
  create_layout,
  geom_edge_link,
  geom_node_point,
  ggraph,
  scale_edge_colour_manual
)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges2)
importFrom(ggstar,geom_star)
importFrom(ggtree,
  geom_text2,
  geom_tiplab,
  geom_tippoint,
  ggtree,
  theme_tree2
)
importFrom(ggtreeExtra,geom_fruit)
importFrom(grDevices,
  col2rgb,
  dev.control,
  dev.off,
  pdf,
  png,
  rainbow,
  recordPlot,
  rgb
)
importFrom(graphics,
  boxplot,
  hist,
  legend,
  mtext
)
importFrom(grid,unit)
importFrom(igraph,
  E,
  V,
  betweenness,
  closeness,
  cluster_fast_greedy,
  cluster_louvain,
  components,
  constraint,
  coreness,
  degree,
  delete_vertex_attr,
  delete_vertices,
  diameter,
  distances,
  ecount,
  edge_density,
  eigen_centrality,
  induced_subgraph,
  is_connected,
  is_weighted,
  mean_distance,
  membership,
  modularity,
  neighbors,
  page_rank,
  read_graph,
  set_vertex_attr,
  strength,
  transitivity,
  vcount,
  vertex_attr_names
)
importFrom(limma,makeContrasts)
importFrom(matrixStats,
  rowMeans2,
  rowMedians
)
importFrom(methods,is)
importFrom(microbiome,
  meta,
  plot_core
)
importFrom(officer,
  docx_summary,
  read_docx
)
importFrom(patchwork,wrap_plots)
importFrom(phangorn,
  bootstrap.phyDat,
  dist.ml,
  phyDat
)
importFrom(phyloseq,
  "otu_table<-",
  "tax_table<-",
  "taxa_names<-",
  filter_taxa,
  merge_phyloseq,
  merge_taxa,
  nsamples,
  otu_table,
  phy_tree,
  phyloseq,
  prune_samples,
  prune_taxa,
  psmelt,
  rarefy_even_depth,
  refseq,
  sample_data,
  sample_names,
  sample_sums,
  subset_taxa,
  tax_glom,
  tax_table,
  taxa_are_rows,
  taxa_names,
  taxa_sums,
  transform_sample_counts
)
importFrom(randomForest,
  importance,
  randomForest
)
importFrom(reshape2,melt)
importFrom(rlang,
  as_name,
  sym
)
importFrom(scales,
  label_scientific,
  rescale
)
importFrom(stats,
  aggregate,
  as.formula,
  median,
  model.matrix,
  na.omit,
  p.adjust,
  quantile,
  reformulate,
  relevel,
  reorder,
  sd,
  setNames,
  wilcox.test
)
importFrom(tibble,
  as_tibble,
  rownames_to_column
)
importFrom(tidyr,
  pivot_longer,
  pivot_wider
)
importFrom(utils,
  capture.output,
  globalVariables,
  install.packages,
  write.csv
)
importFrom(xml2,
  read_xml,
  write_xml,
  xml_attr,
  xml_find_all,
  xml_remove,
  xml_set_attr
)
