_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: docs/intro
parts:
- caption: Helical API Documentation 📚
  chapters:
  - file: docs/Geneformer.rst
  - file: docs/UCE.rst
  - file: docs/scGPT.rst
  - file: docs/hyena_dna.rst
- caption: RNA Tutorials🪄
  chapters:
  - file : examples/notebooks/Geneformer-vs-UCE
  - file: examples/notebooks/Quick-Start_Tutorial
  - file: examples/notebooks/Cell-Type-Annotation
- caption: DNA Tutorials🪄
  chapters:
  - file: examples/notebooks/Hyena-DNA-Inference
- caption: Fine-Tuning 🎛️
  chapters:
  - file: examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
- caption: Benchmarking 📊
  chapters:
  - file: docs/benchmarking/description
  # - file : examples/geneformer_example

# - caption: Basic examples 🪄
#   chapters:
#   - file: markdown
#   - file: notebooks
#   - file: markdown-notebooks
# - caption: Cool extensions 🕶️
#   chapters:
#   - file: intersphinx
#   - file: sphinx-examples
#   - file: sphinx-hoverxref
#   - file: sphinx-proof