mkdocs.yml

site_name: GWASTutorial
site_author: HE Yunye
# Canonical URL for GitHub Pages (project site). Change if you use a fork or custom domain.
site_url: https://cloufield.github.io/GWASTutorial/
repo_name: 'GitHub'
repo_url: https://github.com/Cloufield/GWASTutorial
edit_uri: ""
copyright: "GWASTutorial is licensed under the MIT license"
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nav:
    - Home: 
      - "Tutorial guide" : index.md
      - "Prerequisite Knowledge" : basics.md
      - "Introduction" : 00_Introduction.md
      - "Overview" : 39_overview.md
      - "About" : 99_About.md
      - "Update Log" : 98_updatelog.md
    - "Command Line" :
       - "Programming for GWAS" : 89_programming.md
       - "Linux" : 
          - "Linux Basics" : 02_Linux_basics.md
          - "Windows Linux Subsystem" : 82_windows_linux_subsystem.md
          - "SSH" : 84_ssh.md
          - "Job scheduler" : 85_job_scheduler.md
          - "Text editing - awk" : 60_awk.md
          - "Text editing - sed" : 61_sed.md
          - "Linux Resources" : 69_resources.md
       - "Python":
          - "Python Basics": 70_python_basics.md
          - "Python Resources" : 71_python_resources.md
          - "Anaconda" : 80_miniconda.md
          - "Jupyter notebook" : 81_jupyter_notebook.md
       - "R" : 
          - "R Basics": 75_R_basics.md
          - "R Resources" : 76_R_resources.md
       - "Other tools" :
          - "Git and github" : 83_git_and_github.md
    - "Pre-GWAS" :
       - "1000 Genomes Project" : 40_1000_genome_project.md
       - "Sample Dataset" : 01_Dataset.md
       - "Data Formats" : 03_Data_formats.md
       - "Genotype Data QC" : 04_Data_QC.md
       - "Sample PCA" : 05_PCA.md
       - "PCA Visualization" : plot_PCA.md
       - "Phasing" : Phasing.md
       - "Imputation": Imputation.md
    - "GWAS" : 
       - "Association tests by PLINK": 06_Association_tests.md
       - "Visualization by gwaslab": Visualization.md
       - "Linear mixed model (LMM)" : 33_linear_mixed_model.md
       - "Saddlepoint approximation by SAIGE" : 35_saddlepoint_approximation.md
       - "Whole genome regression by REGENIE" : 32_whole_genome_regression.md
       - "Rare variant association tests" : 34_rare_variant.md

    - "Post-GWAS" :
       - "Post-GWAS Analysis Overview" : 29_postgwas.md
       - "Annotation by ANNOVAR & VEP" : 07_Annotation.md
       - "SNP-heritability estimation by GREML" : 14_gcta_greml.md
       - "LD score regression by LDSC" : 08_LDSC.md
       - "Gene/Gene-set tests by MAGMA" : 09_Gene_based_analysis.md
       - "Fine-mapping by susieR" : 
          - "Fine-mapping Basics" : 12_fine_mapping.md
          - "SuSIE Fine-mapping Tutorial" : finemapping_susie.md
       - "Meta-analysis" : 11_meta_analysis.md
       - "Polygenic Risk Score" : 
          - "PRS Basics" : 10_PRS.md
          - "PRS evaluation" : PRS_evaluation.md
       - "Mendelian randomization": 
          - "MR Basics" : 16_mendelian_randomization.md
          - "TwoSampleMR Tutorial" : TwoSampleMR.md
       - "Conditional analysis" : 18_Conditioning_analysis.md
       - "Colocalization" : 17_colocalization.md
       - "TWAS (using FUSION)": 21_twas.md
       - "Single-cell genomics integration": 25_singlecell.md
    - Topics :
       - "Allele" : 36_alleles.md
       - "Linkage Disequilibrium (LD)" : 19_ld.md
       - "Heritability Concepts" : 13_heritability.md
       - "Statistical power" : 20_power_analysis.md
       - "Winner's curse" : 15_winners_curse.md
       - "Bias" : 22_bias.md
       - "Relatedness and sample structure" : 28_relatedness.md
       - "Phenotype normalization" : 26_normalization.md
       - "Measure of effect" : 55_measure_of_effect.md
       - LiftOver:
         - "Coordinate Systems" : 38_coordinate_system.md
         - "Liftover" : 37_liftover.md
         - "UCSC LiftOver Tool" : LiftOver.md
    - "Assignments" :
       - "Assignment - 1KG PCA" : 95_Assignment.md
       - "Assignment - Presentation" : 96_Assignment2.md
    - "Recommended reading" :
       - "Overview" : 90_Recommended_Reading.md

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extra_css:
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plugins:
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