_site.yml

name : "SGA"
title : "Statistical Genomics Analysis (SGA)"
navbar:
  title: "SGA"
  left:
    - icon: fa-home
      href: index.html
      
    - text: "Lectures"
      icon: fa-chalkboard-teacher
      menu:
      - text: ---- INTRODUCTION ----
      - text: 1.1 Position
        href: intro.html
      - text: 1.2 Recap linear model
        href: recapGeneralLinearModel.html
      - text: ---- MODULE I PROTEOMICS ----
      - text: 1.1 MS Basics
        href: ./figs/part1_ms_basics.pdf
      - text: 1.2 Identification
        href: ./figs/part1_ms_basics.pdf
      - text: 2.1 Identification - FDR - QC
        href: TargetDecoy.html
      - text: 2.2.1 Quantification - Preprocessing
        href: pda_quantification_preprocessing.html
      - text: 2.2.2 Wrap-up Preprocessing - Peptide-Level-Models
        href: pda_robustSummarisation_peptideModels.html
      - text: 2.3.1 Quantification - Differential Abundance Analysis
        href: pda_quantification_inference.html
      - text: 2.3.2. Wrap-up DA - Blocking
        href: pda_blocking_wrapup.html
      - text: 2.3.3. Technical Details
        href: pda_technicalDetails.html
      - text: ---- MODULE II RNA-seq ----
      - text: 1.  Introduction to RNA-seq
        href: sequencing_intro.html
      - text: 2.  Working with count data and GLMs
        href: sequencing_countData.html
      - text: 3.  Technical Details
        href: sequencing_technicalDE.html
      - text: 4. Transcript-level DE and Usage
        href: https://www.biorxiv.org/content/10.1101/2023.06.29.547014v2
      - text: 6. Intro to scRNA-seq
        href: sequencing_singleCell.html

        
    - text: "tutorials"
      icon: fa-laptop
      menu:
      - text: ---- INTRODUCTION ----
      - text: 1 Intro KPNA2
        href: multipleRegression_KPNA2.html
      - text: ---- MODULE I PROTEOMICS ----
      - text: 1. Bioinformatics for Proteomics
        href: https://www.compomics.com/bioinformatics-for-proteomics/
      - text: 2.1. Target Decoy QC
        href: TargetDecoyTutorial.html
      - text: 2.2. Quantification - Preprocessing
        href: pda_tutorialPreprocessing.html
      - text: 2.3. Quantification - Design
        href: pda_tutorialDesign.html   
      - text: 1. Read mapping 
        href: sequencingTutorial1_mapping.html
      - text: 2. Working with Count Data
        href: sequencingTutorial2_DE.html
      - text: 4. Transcript-level DE and Usage
        href: sequencingTutorial3_DE.html
      - text: 6. Tutorial scRNA-seq
        href: scRNA-seq-Tutorial.html

 
right:
    - icon: fab fa-github      
      href: https://github.com/statOmics/SGA
    - text: "statOmics"
      href: http://statomics.github.io/
      
output_dir: "docs"

output:
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      code_download: true
      theme: cosmo
      toc: true
      toc_float: true
      highlight: tango
      number_sections: true
      df_print: paged
new_session: true
exclude: ["install.R"]