_pkgdown.yml

url: https://rbioapi.moosa-r.com

home:
  title: "User-Friendly R Interface to Biologic Web Services' API"
  description: "Connect to Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt in R with rbioapi package."

template:
  bootstrap: 5
  bootswatch: cosmo
  params:
    ganalytics: G-BF9VGFNZ4C

authors:
  Moosa Rezwani:
    href: https://moosa-r.com/

navbar:
  bg: secondary
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    - news
    right:
    - search
    - github
    - portfolio
  components:
    reference:
      text: Functions
      href: reference/index.html
    news:
      text: News
      href: news/index.html
    intro:
      text: Get Started
      href: articles/rbioapi.html
    articles:
      text: Articles & Supported Services
      menu:
      - text: 'rbioapi: Get Started'
        href: articles/rbioapi.html
      - text: ----
      - text: 'Enrichr & rbioapi'
        href: articles/rbioapi_enrichr.html
      - text: 'JASPAR & rbioapi'
        href: articles/rbioapi_jaspar.html
      - text: 'miEEA & rbioapi'
        href: articles/rbioapi_mieaa.html
      - text: 'PANTHER & rbioapi'
        href: articles/rbioapi_panther.html
      - text: 'Reactome & rbioapi'
        href: articles/rbioapi_reactome.html
      - text: 'STRING & rbioapi'
        href: articles/rbioapi_string.html
      - text: 'UniProt & rbioapi'
        href: articles/rbioapi_uniprot.html
      - text: ----
      - text: 'Do with rbioapi: Over-Representation (Enrichment) Analysis in R'
        href: articles/rbioapi_do_enrich.html
    github:
      icon: fab fa-github fa-lg
      href: https://github.com/moosa-r/rbioapi/
      aria-label: GitHub
    portfolio:
      icon: fa-solid fa-id-card
      href: https://moosa-r.com/
      aria-label: Moosa Rezwani Portfolio Website

reference:
- title: "Helper functions"
  desc: >
    Functions that assist you with the overall experience of rbioapi
  contents:
    - rba_options
    - rba_connection_test
    - rba_pages

- title: Enrichr (rba_enrichr_*)
  desc: >
    Functions that connect you to [Enrichr](https://maayanlab.cloud/Enrichr/)
    (Gene list enrichment analysis tool) API resources.

  contents:
    - starts_with("rba_enrichr")

- title: JASPAR (rba_jaspar_*)
  desc: >
    Functions that connect you to [JASPAR](https://jaspar.elixir.no/)
    (Database of transcription factor binding profiles) API resources.
  contents:
    - starts_with("rba_jaspar")

- title: miEAA (rba_mieaa_*)
  desc: >
    Functions that connect you to [miEAA](https://ccb-compute2.cs.uni-saarland.de/mieaa2/)
    (miRNA Enrichment Analysis and Annotation Tool) API resources.
  contents:
    - starts_with("rba_mieaa")

- title: PANTHER (rba_panther_*)
  desc: >
    Functions that connect you to [PANTHER](https://www.pantherdb.org/)
    (Protein Analysis THrough
    Evolutionary Relationships) API resources.
  contents:
    - starts_with("rba_panther")

- title: Reactome Analysis Services (rba_reactome_*)
  desc: >
    Functions that connect you to [Reactome](https://reactome.org/)
    pathway database's Analysis services API resources.
  contents:
    - starts_with("rba_reactome_analysis")

- title: Reactome Contents Services (rba_reactome_*)
  desc: >
    Functions that connect you to [Reactome](https://reactome.org/)
    pathway database's Contents Services API resources.
- subtitle: Database Info Queries
  contents:
    - rba_reactome_version
- subtitle: Disease Related Queries
  contents:
    - rba_reactome_diseases
- subtitle: Physical Entity Queries
  contents:
    - starts_with("rba_reactome_complex")
    - rba_reactome_participant_of
    - rba_reactome_entity_other_forms
- subtitle: Queries Related to Events
  contents:
    - starts_with("rba_reactome_event")
- subtitle: Format Exporter
  contents:
    - starts_with("rba_reactome_exporter")
- subtitle: Molecule Interactors
  contents:
    - starts_with("rba_reactome_interactors")
- subtitle: Mapping Related Queries
  contents:
    - rba_reactome_mapping
- subtitle: Orthology Related Queries
  contents:
    - rba_reactome_orthology
- subtitle: Queries Related to Participants
  contents:
    - rba_reactome_participants
- subtitle: Pathway Related Queries
  contents:
    - starts_with("rba_reactome_pathways")
- subtitle: Person Queries
  contents:
    - starts_with("rba_reactome_people")
- subtitle: Common Data Retrieval
  contents:
    - rba_reactome_query
- subtitle: ReferenceEntity Queries
  contents:
    - rba_reactome_xref
- subtitle: Species Related Queries
  contents:
    - rba_reactome_species

- title: STRING (rba_string_*)
  desc: >
    Functions that connect you to [STRING](https://string-db.org/)
    (Functional protein association networks) API resources.
  contents:
    - starts_with("rba_string")

- title: UniProt (rba_uniprot_*)
  desc: >
    Functions that connect you to [UniProt](https://www.uniprot.org/) (Universal Protein Resource)
    API resources.
- subtitle: "Proteins - Proteins"
  contents:
    - starts_with("rba_uniprot_antigens")
    - starts_with("rba_uniprot_epitope")
    - starts_with("rba_uniprot_features")
    - starts_with("rba_uniprot_mutagenesis")
    - starts_with("rba_uniprot_proteins")
    - starts_with("rba_uniprot_rna_edit")
    - starts_with("rba_uniprot_variation")
- subtitle: "Proteomics"
  contents:
    - starts_with("rba_uniprot_proteomics")
    - starts_with("rba_uniprot_ptm")
- subtitle: "Proteomes"
  contents:
    - starts_with("rba_uniprot_proteomes")
    - starts_with("rba_uniprot_genecentric")
- subtitle: "Taxonomy"
  contents:
    - starts_with("rba_uniprot_taxonomy")
- subtitle: "Coordinates"
  contents:
    - starts_with("rba_uniprot_coordinates")
- subtitle: "Uniparc"
  contents:
    - starts_with("rba_uniprot_uniparc")