myst.yml

# See docs at: https://mystmd.org/guide/frontmatter
version: 1
site:
  template: book-theme
  # options:
  #   favicon: favicon.ico
  #   logo: site_logo.png

project:
  toc:
    # Auto-generated by `myst init --write-toc`
    - file: README.md

    - file: docs/INTRODUCTION.md
    - file: docs/UNDERSTAND.md
    - file: docs/DOWNLOAD.md
    - file: docs/QC_META.md
    - file: docs/QC_READS.md
    - file: docs/PREPROCESS_READS.md
    - file: docs/QC_MAT.ipynb
    - file: docs/PREPROCESS_MAT.ipynb
    - file: docs/TOOLS.md
      # children:
      #   - title: Atac 10xatac
      #     children:
      #       - file: examples/atac-10xatac/preprocess.ipynb
      #       - file: examples/atac-10xatac/qc.ipynb
      #   - title: Atac 10xmultiome
      #     children: 
      #       - file: examples/atac-10xmultiome/preprocess.ipynb
      #       - file: examples/atac-10xmultiome/qc.ipynb
      #   - title: Crispr 10xcrispr
      #     children:
      #       - file: examples/crispr-10xcrispr/preprocess.ipynb
      #       - file: examples/crispr-10xcrispr/qc.ipynb
      #   - title: Multi Dogmaseq Lll
      #     children:
      #       - file: examples/multi-dogmaseq-lll/preprocess.ipynb
      #   - title: Rna 10xv3
      #     children:
      #       - file: examples/rna-10xv3/preprocess.ipynb
      #       - file: examples/rna-10xv3/qc.ipynb
      #   - title: Rna 10xv3 Nuclei
      #     children:
      #       - file: examples/rna-10xv3-nuclei/preprocess.ipynb
      #       - file: examples/rna-10xv3-nuclei/qc.ipynb
      #   - title: Rna Splitseq
      #     children:
      #       - file: examples/rna-splitseq/preprocess.ipynb
      #       - file: examples/rna-splitseq/qc.ipynb
      #   - title: Rna Visium Spatial
      #     children:
      #       - file: examples/rna-visium-spatial/preprocess.ipynb
      #       - file: examples/rna-visium-spatial/qc.ipynb
      #   - title: Tag Clicktag
      #     children:
      #       - file: examples/tag-clicktag/preprocess.ipynb
      #       - file: examples/tag-clicktag/qc.ipynb