annsql/mkdocs.yml at main · ArpiarSaundersLab/annsql · GitHub

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site_name: AnnSQL Docs
nav:
  - Home: index.md
  - Installation: install.md
  - Tutorials:
    - Basic Usage: basic_usage.ipynb
    - On-Disk: build_ondisk_database.ipynb
    - In-Memory: build_in_memory_database.ipynb
    - Preprocessing: preprocessing.ipynb
    - Differential Expression: de.ipynb
    - Meta Cells: build_meta_cells.ipynb
    - R usage: R_usage.md
  # - Usage:
  #   - Backup UMI Counts: ""
  #   - Build Meta Cells: ""
  #   - Differential Expression: ""
  #   - Export to AnnData: ""
  #   - Filter by Cells: ""
  #   - Filter by Genes: ""
  #   - Highly Variable Genes: ""
  #   - Leiden Clustering: ""
  #   - Marker Genes: ""
  #   - Normalize Counts: ""
  #   - PCA: ""
  #   - Query: ""
  #   - Query Delete: ""
  #   - Query Raw: ""
  #   - Total Counts: ""
  #   - Total Gene Counts: ""
  #   - Transform Expression: ""
  #   - UMAP: ""
  # - Plotting:
  #   - Gene Counts: ""
  #   - UMI Counts: ""
  #   - Principle Components: ""
  #   - PCA Variance: ""
  #   - Highly Variable Genes: ""
  #   - UMAP: ""
  #   - Marker Genes: ""
  - Interoperability: interoperability.md
  - API:
    - AnnSQL: api_annsql.md
    - MakeDb: api_makedb.md
    - BuildDb: api_builddb.md
  - Reference: cite.md
  - Github: "https://github.com/ArpiarSaundersLab/annsql"
plugins:
    - mkdocs-jupyter:
          theme: dark
          ignore_h1_titles: True
    - mkdocstrings:
        handlers:
          python:
            setup_commands:
              - import sys
              - sys.path.append("src")
theme:
    name: material
    palette:
        scheme: slate