_pkgdown.yml

url: https://snystrom.github.io/dremeR/

destination: docs

template:
  params:
    bootswatch: flatly

navbar:
  components:
    articles:
      text: Articles
      menu:
      - text: Install MEME
        href: articles/install_guide.html
      - text: De-Novo Motif Discovery
        href: articles/core_dreme.html
      - text: Motif Comparison
        href: articles/core_tomtom.html
      - text: Motif Enrichment
        href: articles/core_ame.html
      - text: Motif Scanning
        href: articles/core_fimo.html
      - text: Motif Manipulation
        href: articles/tidy_motifs.html
      - text: ChIP-Seq Data Analysis
        href: articles/integrative_analysis.html

articles:
- title: Core Utilities
  contents:
  - starts_with("core_")
- title: Examples
  contents:
  - tidy_motifs
  - integrative_analysis
- title: Help & Troubleshooting
  contents:
  - install_guide

reference:
- title: Core Tools
  contents:
  - runStreme
  - runDreme
  - runMeme
  - runTomTom
  - runAme
  - runFimo

- title: Utilities
  contents:
  - check_meme_install
  - meme_is_installed
  - get_sequence
  - add_sequence
  - write_fasta

- title: Data Visualization
  contents:
  - view_tomtom_hits
  - plot_sequence_heatmap
  - plot_ame_heatmap
  - ame_compare_heatmap_methods

- title: Motif Manipulation
  contents:
  - remove_duplicate_motifs
  - has_duplicate_motifs

- title: Data Helpers
  contents:
  - force_best_match
  - update_best_match
  - drop_best_match
  - nest_tomtom

- title: Data Import
  contents:
  - importStremeXML
  - importDremeXML
  - importTomTomXML
  - importAme
  - importFimo
  - importMeme

- title: Example Datasets
  contents:
  - starts_with("example_")