_pkgdown.yml

destination: docs
template:
  params:
    bootswatch: united
    docsearch:
      api_key: 7f13d388d59fea08d4add29291ea2896
      index_name: pathfindr
url: https://egeulgen.github.io/pathfindR/
news:
- one_page: false
reference:
  - title: "pathfindR"
    desc: >
      pathfindR package
    contents:
      - pathfindR
  - title: "Main functions"
    desc: >
      Main functions of pathfindR
    contents:
      - run_pathfindR
      - cluster_enriched_terms
      - enrichment_chart
      - score_terms
      - plot_scores
      - term_gene_heatmap
      - term_gene_graph
      - UpSet_plot
      - visualize_terms
      - cluster_graph_vis
      - visualize_active_subnetworks
  - title: "Data Generation"
    desc: >
      Functions to generate PIN and gene sets data
    contents:
      - get_pin_file
      - get_gene_sets_list
  - title: "Comparison of 2 pathfindR Results"
    desc: >
      Functions to compare 2 different pathfindR results
    contents:
      - combine_pathfindR_results
      - combined_results_graph
  - title: "Enrichment-related functions"
    desc: >
      Active subnetwork search- and Enrichment-related functions
    contents:
      - active_snw_enrichment_wrapper
      - single_iter_wrapper
      - active_snw_search
      - annotate_term_genes
      - enrichment
      - enrichment_analyses
      - fetch_gene_set
      - filterActiveSnws
      - hyperg_test
      - input_processing
      - input_testing
      - return_pin_path
      - summarize_enrichment_results
  - title: "Clustering-related functions"
    desc: >
      Clustering-related functions
    contents:
     - create_kappa_matrix
     - fuzzy_term_clustering
     - hierarchical_term_clustering
  - title: "Visualization functions"
    desc: >
      Visualization-related functions
    contents:
      - color_kegg_pathway
      - visualize_KEGG_diagram
      - visualize_term_interactions
  - title: "Misc. functions"
    desc: >
      Miscellaneous functions
    contents:
      - configure_output_dir
      - check_java_version
      - fetch_java_version
      - get_biogrid_pin
      - process_pin
      - get_kegg_gsets
      - get_reactome_gsets
      - get_mgsigdb_gsets
      - gset_list_from_gmt
      - create_HTML_report
      - isColor