update index week 3

_site.yml

@@ -14,13 +14,35 @@ navbar:
         href: intro.html
       - text: 1.2 Recap linear model
         href: recapGeneralLinearModel.html
+            - text: ---- MODULE I PROTEOMICS ----
+      - text: 1. Proteomics Bioinformatics
+        href: docs/martens_proteomics_bioinformatics.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: "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   
 
 right:
     - icon: fab fa-github      

index.Rmd

@@ -59,7 +59,7 @@ source("https://raw.githubusercontent.com/statOmics/SGA/master/install.R")
    - Tutorial KPNA2: [HTML](./multipleRegression_KPNA2.html),  [PDF](./multipleRegression_KPNA2.pdf)
    - link to a compressed figures directory: [download figures](https://raw.githubusercontent.com/statOmics/SGA/master/figures.tar.gz)
 
-<!--
+
 
 ## Module I: Proteomics Data Analysis (Week 1-5)
 
@@ -86,6 +86,8 @@ source("https://raw.githubusercontent.com/statOmics/SGA/master/install.R")
   - Lecture Differential Abundance Analysis: [html](./pda_quantification_inference.html), [pdf](./pda_quantification_inference.pdf)
   - Tutorial: [Design](pda_tutorialDesign.html)
   - Wrap-up Blocking: [html](./pda_blocking_wrapup.html), [pdf](./pda_blocking_wrapup.pdf)
+
+<!--
   - Solution: [Heart Example](heartMainInteraction.html)
   - Technical Details: [Technical Details](technicalDetailsProteomics.html)