PlantGeneticsCourse/_quarto.yml at main · icarda/PlantGeneticsCourse · GitHub

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project:
  type: book
  output-dir: docs  # Ensures rendered site ends up here for GitHub Actions

book:
  title: "Plant Genetics Data Analysis with R - Baku"
  subtitle: "A Practical Guide for Breeders"
  description: "This book provides a comprehensive introduction to R programming and its application in plant genetic data analysis."
  page-footer:
    left: "Copyright 2025, ICARDA"
    right:
      - icon: github
        href: https://github.com/
      - icon: twitter
        href: https://twitter.com/
  author: "Tamara Ortiz /	Khaled Al-Sham’aa / ICARDA"
  date: today
  date-format: "YYYY-MM-DD"
  chapters:
    - index.qmd
    - part: "Introduction and Setup"
      chapters:
        - 00_Setup_Intro/00_Welcome.qmd
        - 00_Setup_Intro/01_Setup_R_RStudio.qmd
    - part: "R Programming Fundamentals"
      chapters:
        - 01_R_Basics/01_Intro_To_R.qmd
        - 01_R_Basics/02_Data_Types_Structures.qmd
        - 01_R_Basics/03_Basic_Operations.qmd
        - 01_R_Basics/04_Reading_Writing_Data.qmd
        - 01_R_Basics/05_Simple_Plotting.qmd
    - part: "Handling Breeding Data"
      chapters:
        - 02_Data_Handling/01_Loading_Data.qmd
        - 02_Data_Handling/02_Data_QC_Filtering.qmd
        - 02_Data_Handling/03_General_Biostatistics.qmd
    - part: "Core Genomic Concepts"
      chapters:
        - 03_Genomic_Concepts/01_SNPs_Genotypes.qmd
        - 03_Genomic_Concepts/02_Filtering_SNP_Data.qmd
    - part: "Population Structure and Relatedness"
      chapters:
        - 04_Pop_Structure/01_Kinship_Relatedness.qmd
        - 04_Pop_Structure/02_Genetic_Diversity.qmd
        - 04_Pop_Structure/03_Pop_Structure.qmd
        - 04_Pop_Structure/04_Phylo_Tree.qmd
    - part: "Genome Wide Association Studies (GWAS)"
      chapters:
        - 05_GWAS/01_Initial_Concepts.qmd
        - 05_GWAS/02_Single_Trait_GWAS.qmd
    - part: "Genomic Selection"
      chapters:
        - 06_GS/01_Genomic_Selection.qmd

format:
  html:
    theme: cosmo
  pdf:
    documentclass: scrreprt
    toc: true
    toc-depth: 3
  revealjs:
    theme: default
    slide-number: true
    chalkboard: true
    logo: assets/icarda_logo.png
  beamer:
    documentclass: beamer
    theme: Madrid
    colortheme: default
    logo: assets/icarda_logo.png
    slide-level: 2
    aspectratio: 169

bibliography: references.bib

editor: visual