mkdocs.yml

site_name: Bioinformatic Tutorial (Daxing Research)
repo_url: https://github.com/Starlitnightly/bioinformatic_tutorial
edit_uri: edit/main/docs/

nav:
- 写在前面: index.md
- 基础环境配置:
    - 配置1. Python环境: CONFIG/config_1.md
    - 配置2. Linux环境: CONFIG/config_2.md
    - 配置3. R语言环境: CONFIG/config_3.md
- RNA-seq上游分析:
    - 1-1. 环境配置: RNASEQUP/rnasequp_1.md
    - 1-2. 上游分析全教程: RNASEQUP/rnasequp_2.md
- RNA-seq下游分析:
    - 2-1. 环境配置: RNASEQ/rnaseq_1.md
    - 2-2. 差异表达基因(DEG)分析: RNASEQ/rnaseq_2.md
    - 2-3. 通路富集分析(GSEA): RNASEQ/rnaseq_3.md
- 单细胞样本对齐:
    - 3-1. 环境配置: SCGLUE/scglue_1.md
    - 3-2. 数据预处理: SCGLUE/scglue_2.md
    - 3-3. 模型准备: SCGLUE/scglue_3.md
    - 3-4. 模型训练: SCGLUE/scglue_4.md
    - 3-5. 对齐细胞: SCGLUE/scglue_5.md
- MOFA单细胞多组学因子分析:
    - 4-1. 环境配置: MOFA/mofa_1.md
    - 4-2. 单细胞样本对齐: MOFA/mofa_2.md
    - 4-3. scRNA-seq数据处理: MOFA/mofa_3.md
    - 4-4. scATAC-seq数据处理: MOFA/mofa_4.md
    - 4-5. MOFA模型构建: MOFA/mofa_5.md
    - 4-6. MOFA下游分析-R语言环节: MOFA/mofa_6.md
    - 4-7. MOFA下游分析-Python环节: MOFA/mofa_7.md
- TMT蛋白组学分析:
    - 5-1. 环境配置: TMT/tmt_1.md
    - 5-2. TMT蛋白组学上游分析: TMT/tmt_2.md
    - 5-3. TMT蛋白组学下游分析: TMT/tmt_3.md
- 多组学分析:
    - 6-1. 数据准备: MultiOMIC/book-1.md
    - 6-2. GLUE多组学整合: MultiOMIC/book-2.md
    - 6-3. 细胞亚群分析: MultiOMIC/book-3.md
    - 6-4. 差异表达分析: MultiOMIC/book-4.md
    - 6-5. 细胞通讯分析: MultiOMIC/book-5.md
    - 6-6. 动态调控分析: MultiOMIC/book-6.md
    - 6-7. 转录因子网络: MultiOMIC/book-7.md
- Python可视化:
    - 1-1. 火山图: PLOT/plot_1.md
    - 1-2. 箱线图: PLOT/plot_2.md
    - 1-3. 热图(聚类): PLOT/plot_3.md


plugins:
  - mkdocs-jupyter

theme:
  name: material
  custom_dir: docs/overrides

  palette:
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      scheme: default
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/toggle-switch
        name: Switch to light mode

  features:
    - navigation.instant
    - navigation.tracking
    - navigation.indexes

markdown_extensions:
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.highlight:
      linenums: true
      linenums_style: pymdownx-inline
  - pymdownx.superfences:
      custom_fences:
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          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.inlinehilite

extra_javascript:
  - javascripts/config.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js