update course for 2023-2024

statOmics · Sep 19, 2023 · 2483cfb · 2483cfb
1 parent 8175d2d
commit 2483cfb
Show file tree

Hide file tree

Showing 60 changed files with 1,511 additions and 476 deletions.
diff --git a/README.md b/README.md
@@ -1,3 +1,3 @@
-# Statistical Genomics Analysis, 2021-2022
+# Statistical Genomics Analysis, 2023-2024
 
-Course website at https://statomics.github.io/SGA21/.
+Course website at https://statomics.github.io/SGA/.
diff --git a/_site.yml b/_site.yml
@@ -15,54 +15,10 @@ navbar:
       - 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: 2.3.3 Technical Details
-        href: technicalDetailsProteomics.html
-      - text: ---- MODULE I PROTEOMICS ----
-      - text: 1.  Introduction to RNA-seq
-        href: sequencing_intro.html
-      - text: 2.  Working with count data and GLMs
-        href: sequencing_countData.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: ---- MODULE II RNA-seq ----
-      - text: 1. Read mapping 
-        href: sequencingTutorial1_mapping.html
-      - text: 2. Working with Count Data
-        href: sequencingTutorial2_DE.html
-      - text: 3. Single Cell RNA-seq Data Analysis
-        href: scRNA-seq-Tutorial.html
-
-
+
 right:
     - icon: fab fa-github      
-      href: https://github.com/statOmics/SGA21
+      href: https://github.com/statOmics/SGA
     - text: "statOmics"
       href: http://statomics.github.io/
 output:

diff --git a/bibliography.bib b/bibliography.bib
diff --git a/figs/3D_model_hydrogen_bonds_in_water.png b/figs/3D_model_hydrogen_bonds_in_water.png
diff --git a/figs/ATP-ADP.png b/figs/ATP-ADP.png
diff --git a/figs/Amino-acids-and-Proteins.jpeg b/figs/Amino-acids-and-Proteins.jpeg
diff --git a/figs/Aminoacids_table.png b/figs/Aminoacids_table.png
diff --git a/figs/Binary_Fission_2.png b/figs/Binary_Fission_2.png
diff --git a/figs/Brain_regions_in_memory_formation.png b/figs/Brain_regions_in_memory_formation.png
diff --git a/figs/Brain_regions_in_memory_formation_updated.jpeg b/figs/Brain_regions_in_memory_formation_updated.jpeg
diff --git a/figs/Carbohydrates-definition-classification-with-structure-and-functions.jpeg b/figs/Carbohydrates-definition-classification-with-structure-and-functions.jpeg
diff --git a/figs/Cell_membrane_detailed_diagram_4.png b/figs/Cell_membrane_detailed_diagram_4.png
diff --git a/figs/Citric_acid_cycle_with_aconitate_2.png b/figs/Citric_acid_cycle_with_aconitate_2.png
diff --git a/figs/DNA_polymerase.png b/figs/DNA_polymerase.png
diff --git a/figs/Dictyostelida.jpeg b/figs/Dictyostelida.jpeg
diff --git a/figs/Dictyostelida.jpg b/figs/Dictyostelida.jpg
diff --git a/figs/Difference_DNA_RNA-EN.png b/figs/Difference_DNA_RNA-EN.png
diff --git a/figs/DyneinHeavyChainOnMT.png b/figs/DyneinHeavyChainOnMT.png
diff --git a/figs/EnzymePadlockKey.png b/figs/EnzymePadlockKey.png
diff --git a/figs/Holography-reconstruction.png b/figs/Holography-reconstruction.png
diff --git a/figs/I08-13-firststars6.jpeg b/figs/I08-13-firststars6.jpeg
diff --git a/figs/JohnBonnerSlimeMoldMovies.mp4 b/figs/JohnBonnerSlimeMoldMovies.mp4
diff --git a/figs/LichenDiagram.png b/figs/LichenDiagram.png
diff --git a/figs/Meiosis_Stages.png b/figs/Meiosis_Stages.png
diff --git a/figs/Phylogenetic_tree.png b/figs/Phylogenetic_tree.png
diff --git a/figs/Phylogenetic_tree.svg.png b/figs/Phylogenetic_tree.svg.png
diff --git a/figs/RNA-Nucleobases.png b/figs/RNA-Nucleobases.png
diff --git a/figs/animalCell.png b/figs/animalCell.png
diff --git a/figs/convection_cells.png b/figs/convection_cells.png
diff --git a/...twins-with-phenotypic-discordance-due-to-environmental-exposure-Although-MZ.png b/...twins-with-phenotypic-discordance-due-to-environmental-exposure-Although-MZ.png
diff --git a/figs/eichinger2.pdf b/figs/eichinger2.pdf
diff --git a/figs/endosymbiosis.png b/figs/endosymbiosis.png
diff --git a/figs/epigeneticsEnvironmentalStress.jpeg b/figs/epigeneticsEnvironmentalStress.jpeg
diff --git a/figs/fusion.png b/figs/fusion.png
diff --git a/figs/gene.png b/figs/gene.png
diff --git a/figs/granulation_sun.mp4 b/figs/granulation_sun.mp4
diff --git a/figs/granulation_sun.webm b/figs/granulation_sun.webm
diff --git a/figs/hemoglobin.jpeg b/figs/hemoglobin.jpeg
diff --git a/figs/hires.jpeg b/figs/hires.jpeg
diff --git a/figs/holograph-record.png b/figs/holograph-record.png
diff --git a/figs/holography.png b/figs/holography.png
diff --git a/figs/holographySmall.png b/figs/holographySmall.png
diff --git a/figs/lichen.jpeg b/figs/lichen.jpeg
diff --git a/figs/lifeCycleSunflowerTimeLapse.mp4 b/figs/lifeCycleSunflowerTimeLapse.mp4
diff --git a/figs/liferockystartstrip.jpeg b/figs/liferockystartstrip.jpeg
diff --git a/figs/organisationMulticellular.jpeg b/figs/organisationMulticellular.jpeg
diff --git a/figs/origin_of_life_stages.png b/figs/origin_of_life_stages.png
diff --git a/figs/origin_of_life_stages.svg b/figs/origin_of_life_stages.svg
diff --git a/figs/pastelBiodanza.jpg b/figs/pastelBiodanza.jpg
diff --git a/figs/pastelBiodanzaSmall.jpg b/figs/pastelBiodanzaSmall.jpg
diff --git a/figs/plantCell.png b/figs/plantCell.png
diff --git a/figs/pnas.1711842115fig01.jpg b/figs/pnas.1711842115fig01.jpg
diff --git a/figs/pnas.1711842115fig01.webp b/figs/pnas.1711842115fig01.webp
diff --git a/figs/prokaryoteCell.png b/figs/prokaryoteCell.png
diff --git a/figs/selectionNoDirectionDef.jpg b/figs/selectionNoDirectionDef.jpg
diff --git a/figs/selforganisation.jpg b/figs/selforganisation.jpg
diff --git a/figs/telomeres.png b/figs/telomeres.png
diff --git a/figs/transcription_2.jpeg b/figs/transcription_2.jpeg
diff --git a/index.Rmd b/index.Rmd
@@ -25,7 +25,7 @@ This course is oriented towards biologists and bioinformaticians with a particul
 # Prerequisites
 
 The prerequisites for the Statistical Genomics Analysis course are the successful completion of a basic course of statistics that covers topics on data exploration and descriptive statistics, statistical modeling, and inference: linear models, confidence intervals, t-tests, F-tests, anova, chi-squared test.
-The basis concepts may be revisited in the online course at https://statomics.github.io/PSLS/ (English) and in https://statomics.github.io/sbc21/ (Dutch).
+The basis concepts may be revisited in the online course at https://statomics.github.io/PSLS/ (English) and in https://statomics.github.io/sbc/ (Dutch).
 
 In addition, knowledge of programming in `R` is preferred. A primer to `R` and Data visualization in `R` can be found at:
 
@@ -58,7 +58,9 @@ source("https://raw.githubusercontent.com/statOmics/SGA/master/install.R")
    - Lecture: [HTML](./recapGeneralLinearModel.html), [PDF](./recapGeneralLinearModel.pdf)
    - 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)
 
 ### 1. Bioinformatics for proteomics
@@ -112,3 +114,4 @@ source("https://raw.githubusercontent.com/statOmics/SGA/master/install.R")
 - Lecture Intro to scRNA-seq: [html](./sequencing_singleCell.html), [pdf](./sequencing_singleCell.pdf)
 - Tutorial on scRNA-seq: [handout](./scRNA-seq-Tutorial.html)
 
+-->
diff --git a/intro.Rmd b/intro.Rmd