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site_name: Ritchie Lab Documentation

nav:
  - Home: index.md
  - Installation:
    - Overview of LOKI & Biofilter: 01_Installation/00_LokiBiofilterOverview.md
    - Installation: 01_Installation/01_Installation.md
    - Biofilter Arguments: 01_Installation/02_BiofilterArguments.md
    - Biofilter Configuration: 01_Installation/03_Configuration.md
    - Input File Formats: 01_Installation/04_InputFileFormats.md
    - Output File Formats: 01_Installation/05_OutputFileFormats.md
  - Biofilter: 
    - Let's Get Started: 02_Biofilter/00_GettingStarted.md
    - Filtering Examples: 02_Biofilter/01_FilteringExamples.md
    - Annotation Examples: 02_Biofilter/02_AnnotationExamples.md
    - Filtering AND Annotation: 02_Biofilter/03_FilteringFollowedByAnnotationExamples.md
    - Modeling Examples: 02_Biofilter/04_ModelingExamples.md
    - Use Case 01: 02_Biofilter/05_UseCase01.md
    - Use Case 02: 02_Biofilter/06_UseCase02.md
    - Use Case 03: 02_Biofilter/07_UseCase03.md
    - Appendix: 02_Biofilter/99_Appendix.md
  - LOKI:
    - SQL Tutorial: 03_LOKI/00_SQL-Tutorial.md
    - Knowledge Sources: 03_LOKI/01_KnowledgeSources.md
    - SQLite Data Schema: 03_LOKI/02_DataSchema.md
    - Updating LOKI: 03_LOKI/03_UpdatingLOKI.md
    - Adding New Databases: 03_LOKI/04_AddingDatabases.md
    - Simulated Data Examples: 03_LOKI/05_SimulatedDataExamples.md
  - Cite And Contribute:
    - Cite Us!: 04_CiteUs/01_CodeAndReferences.md
    - Submit Feature Request: 04_CiteUs/02_SubmitFeatureRequest.md
    - Collaborate & Contribute: 04_CiteUs/03_CollaborateWithUs.md
  - For Developers: 
    - LOKI Dev: 05_ForDevelopers/01_Loki_docstring.md
    - Biofilter Dev: 05_ForDevelopers/02_Biofilter_docstring.md
    - Code and References: 05_ForDevelopers/04_CodeAndReferences.md
    - Previous Versions (Unsupported): 05_ForDevelopers/03_DeprecatedVersions.md

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