mkdocs.yaml

# Project Information
site_name: Lab note for UMD BIOI611
site_author: Shaojun Xie 
site_description: >-
  Lab note for BIOI611

# Repository
repo_name: Bix4UMD/BIOI611_lab
repo_url: https://github.com/Bix4UMD/BIOI611_lab.git 
#edit_uri: https://github.com/Bix4UMD/BIOI611_lab/edit/main/docs/

# Copyright
copyright: Copyright © 2024 Shaojun Xie

theme:
  name: readthedocs
  highlightjs: true
  hljs_languages:
    - yaml
    - rust

# Customization
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/Bix4UMD

markdown_extensions:
  - pymdownx.arithmatex:
      generic: true

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

# Page Tree
nav:
  
  - Get ready for the course: 
    - Basic Linux:  basic_linux.md

  - Bulk RNA-seq:
    - Read QC and alignment: bulkRNAseq_lab.md
    - Phred score in FASTQ: Phred_FQ.md
    - Minimal R Introduction: BIOI611_introR.md
    - DEG analysis using DESeq2: BIOI611_DESeq2_analysis.md  
    - DE analysis at isoform-leve using ballgown (example data): BIOI611_ballgown_example.md
    - DE analysis at isoform-leve using ballgown (C. ele data): BIOI611_bulkRNA_SE_ballgown.md 
    - Long read transcriptome: BIOI611_long_read_transcriptome.md
  - scRNA-seq:
    - Initial analysis of 10x scRNA-seq data for human PBMC using cellranger: BIOI611_analysis_10x_dataset_PBMC.md 
    - Downstream analysis of 10x scRNA-seq data for human PBMC using Seurat: BIOI611_scRNA.md
    -  Initial analysis of 10x scRNA-seq data for C. elegans using cellranger: BIOI611_scRNA_seq_cele_cellranger.md
    - Downstream analysis of 10x scRNA-seq data for C. elegans data: BIOI611_scRNA_cele.md
    - Downstream analysis - trajectory analysis using Monocle3: bioi611_monocle_cele.md
      #- Basic R:      basic_r.md
    #- Basic Python: basic_python.md
   
    #- Intronduction:
    #- RNA-seq data analysis: s1_lab_RNAseq_lab.md 

 #- FAQ:
 #     - General Questions: general-questions.md
 #     - Troubleshooting: troubleshooting.md
 #- Reference: ref.md
 # - License: license.md