_toc.yml

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

format: jb-book
root: intro
parts:
  - caption: INTRODUCTION
    chapters:
      - file: notebooks/getting_started
      - file: notebooks/general_accessing_10x_snRNASeq_tutorial
      - file: notebooks/abc_atlas_selection_example
  - caption: DATA 
    chapters:
    - file: descriptions/WMB_dataset
      sections:
      - file: descriptions/WMB-10Xv2
      - file: descriptions/WMB-10Xv3
      - file: descriptions/WMB-10XMulti
      - file: descriptions/WMB-10X
      - file: descriptions/WMB-taxonomy
      - file: descriptions/MERFISH-C57BL6J-638850
      - file: descriptions/MERFISH-C57BL6J-638850-imputed
      - file: descriptions/WMB-neighborhoods
      - file: descriptions/Allen-CCF-2020
      - file: descriptions/MERFISH-C57BL6J-638850-CCF
    - file: descriptions/Zeng_Aging_Mouse_dataset
      sections:
        - file: descriptions/Zeng_Aging_Mouse_10Xv3
        - file: descriptions/Zeng_Aging_Mouse_clustering
        - file: descriptions/Zeng_Aging_Mouse_taxonomy
    - file: descriptions/Zhuang_dataset
      sections:
      - file: descriptions/Zhuang-ABCA-1
      - file: descriptions/Zhuang-ABCA-2
      - file: descriptions/Zhuang-ABCA-3
      - file: descriptions/Zhuang-ABCA-4
    - file: descriptions/WHB_dataset
      sections:
        - file: descriptions/WHB-10Xv3
        - file: descriptions/WHB-10X-clustering
        - file: descriptions/WHB-taxonomy

  - caption: NOTEBOOKS
    chapters:
    - file: descriptions/notebook_subtitle1
      sections:
      - file: notebooks/cluster_annotation_tutorial
      - file: descriptions/notebook_subtitle2
        sections:
        - file: notebooks/10x_snRNASeq_tutorial_part_1
        - file: notebooks/10x_snRNASeq_tutorial_part_2a
        - file: notebooks/10x_snRNASeq_tutorial_part_2b
      - file: descriptions/notebook_subtitle3
        sections:
          - file: notebooks/merfish_tutorial_part_1
          - file: notebooks/merfish_tutorial_part_2a
          - file: notebooks/merfish_tutorial_part_2b
          - file: notebooks/merfish_imputed_genes_example.ipynb
      - file: notebooks/cluster_groups_and_embeddings_tutorial
      - file: notebooks/cluster_neighborhood_gallery
      - file: notebooks/ccf_and_parcellation_annotation_tutorial
      - file: notebooks/merfish_ccf_registration_tutorial
    - file: descriptions/Zeng_Aging_Mouse_notebooks
      sections:
        - file: notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation
        - file: notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial
    - file: descriptions/notebook_subtitle4
      sections:
      - file: notebooks/zhuang_merfish_tutorial
    - file: descriptions/WHB_notebooks
      sections:
      - file: notebooks/WHB_cluster_annotation_tutorial
      - file: notebooks/WHB-10x_snRNASeq_tutorial_part_1
      - file: notebooks/WHB-10x_snRNASeq_tutorial_part_2

  - caption: ADDITIONAL RESOURCES
    chapters:
    - file: docs/README
      sections:
      - file: docs/gene_lists/README
      - file: docs/cluster_annotations/README
      - file: docs/parcellation_annotations/README