Merge branch '2024.04' of github.com:maxplanck-ie/Rintro into 2024.04

.github/workflows/render-qmd.yml

@@ -0,0 +1,84 @@
+name: Rintro2HTML
+run-name: ${{ github.actor }} is testing
+
+on:
+  push:
+    branches: ["2024.04"] 
+
+
+jobs:
+
+  build:
+    name: Conda Tests
+    runs-on: ubuntu-latest
+    defaults:
+       run:
+         shell: bash -l {0}
+    container: node:latest
+
+    steps:
+      - name: Print shell information
+        run: |
+          echo "Shell: $SHELL"
+          echo "Shell version: $($SHELL --version)"
+          uname -a || true
+
+      - uses: actions/checkout@v2
+      - name: Check yaml
+        run: |
+          cat configs/conda.yml || true
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@main
+        with:
+          environment-file: configs/conda.yml
+
+      - name: List Available Environment
+        shell: bash -l {0}
+        run: micromamba list
+
+      - name: Activate Environment
+        run: micromamba activate Rintro
+
+      - name: Check Installation
+        run: |
+          echo "after conda activate Rintro: PATH=$PATH;"
+          which R || true
+          R --version || true
+
+      - name: Installation non-conda packages 
+        run: |
+          Rscript -e 'install.packages(c("dslabs","KernSmooth"), repos="https://cloud.r-project.org")'
+
+      - name: Inspect dslabs ext_data
+        run: |
+          Rscript -e '.libPaths()'
+          Rscript -e 'find.package("dslabs")'
+          Rscript -e 'list.files(system.file(package="dslabs"))'
+          Rscript -e 'list.files(system.file("extdata", package="dslabs"))'           
+
+      - name: Render quarto
+        continue-on-error: true # only for error tracking
+        run: |
+          ls -Rl /github/home/micromamba/envs/Rintro/lib/R/library/dslabs
+          quarto render qmd
+
+      - name: Show all files
+        run: ls -Ral
+
+      - name: Upload
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs
+
+  deploy:
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+

.gitignore

@@ -8,7 +8,9 @@ rmd/*_cache/
 rmd/*_files
 rmd/*RData
 rmd/_site
-<<<<<<< HEAD
 rmd/*.csv
 rmd/*.csv.gz
 .DS_Store
+/.quarto/
+**_files
+**_cache

README.md

@@ -1,11 +1,11 @@
-# Rintro 2023
+# Rintro 2024
 
 This repository contains material for our course: Introduction to R-language.
 
 This branch can be downloaded as zip archive (using the `Code` button above) or cloned such:
 
 ```{bash}
-git clone -b 2023.03 [email protected]:maxplanck-ie/Rintro.git
+git clone -b 2024.04 [email protected]:maxplanck-ie/Rintro.git
 ```
 
 # For participants
@@ -24,13 +24,16 @@ Pre-requisites:
 To setup all required packages run the following in the repo root:
 
 ```{bash}
-mamba env create -f conda_config.yml  
-conda activate Rintro2023
+mamba env create -f configs/conda.yml  
+conda activate Rintro
+
+# dslabs cannot be conda installed
+Rscript -e 'install.packages(c("dslabs","KernSmooth"), repos="https://cloud.r-project.org")'
 ```
 
-To render all material into a full web site under `rmd/_site` run
+To render all material into a full web site under `docs` run
 ```{bash}
-Rscript -e "rmarkdown::render_site('rmd')" 
+quarto render qmd
 ```
 
 The same is available also here: https://maxplanck-ie.github.io/Rintro/

_quarto.yml

@@ -0,0 +1,49 @@
+project:
+  type: website
+  output-dir: docs
+
+website:
+  title: "Rintro 2024"
+
+  navbar:
+    left: 
+      - text: "Modules"
+        icon: book
+        href: qmd/index.qmd
+    right:
+      - text: "GitHub"
+        icon: fa-github
+        href: https://github.com/maxplanck-ie/Rintro/tree/2024.04
+
+
+  page-footer: 
+    left: |
+        Bioinfo Core @ MPI-IE Freiburg (2024) 
+    right:
+      - icon: github
+        href: https://github.com/maxplanck-ie
+
+#    background: "grey"
+format:
+  html:
+    theme: 
+      dark: darkly
+      light: cosmo
+    css: styles.css
+    code-tools: true
+    code-line-numbers: false
+    code-link: false
+    code-fold: true
+    code_folding: hide
+    highlight-style: github
+    highlight: textmate 
+    toc: true
+    toc_depth: 1
+    toc_float: true
+    df_print: paged
+
+execute:
+  freeze: auto
+
+editor: visual
+

conda_config.yml → configs/conda.yml

@@ -1,17 +1,18 @@
-name: Rintro2023
+name: Rintro
 channels:
   - conda-forge
   - bioconda
   - R
   - defaults
 dependencies:
-  - r-base=4.1.3
-  - r-rprojroot=2.0.3
-  - r-markdown=1.5
-  - r-essentials~=4.1
-  - r-rmarkdown=2.14
-  - r-tidyverse=1.3.1
+  - quarto=1.4
+  - r-base=4.2.3
+  - r-tidyverse=2.0.0
   - r-pheatmap=1.0.12
   - r-codetools=0.2.19
   - r-upsetr=1.4.0
   - r-kernsmooth=2.23.20
+  - r-ggridges=0.5.6
+  - r-ggrepel=0.9.4
+  - r-ggthemes=5.1.0
+  - r-kernsmooth=2.23

qmd/00_Introduction.qmd

@@ -0,0 +1,83 @@
+---
+title: "00: Introduction"
+author: "Thomas Manke"
+---
+
+### Block 1: Groundwork
+* Starting RStudio: a GUI for R
+* Simple functions (input, output, parameters & help)
+* Data: I/O, Types, Formats & Structures
+
+### Block 2: Speaking about Data 
+* Data Descriptions
+* Data Visualization: simple plots and advanced heatmaps
+* Data Models: linear models
+
+### Block 3: Open the universe
+* installing and using packages
+* tidyverse: data cleaning, filtering, merging
+
+### Block 4: Advanced topics and case studies
+* R scripts, R markdown & reproducible analyses
+* data exploration
+
+
+
+***
+
+# Goals: 
+After the course you will be able to
+
+* understand the basic syntax of R
+* find help for more nifty problems
+* install and use packages for your specific questions
+* see the limitations of EXCEL
+* understand the importance of structured data
+* understand some bioinformatics jargon
+* understand common difficulties in data analysis
+* increase the value of your CV
+* produce figures such as
+
+![Typical examples from R.](images/sample_plots.png)
+
+[//]: # http://www.r-graph-gallery.com/all-graphs/
+
+***
+
+# Non-Goals:
+This course does *not* teach 
+
+* programming new tools: focus on existing tools
+* bioinformatics: BSc course (3 yrs ++)
+* NGS analysis: other programs (Linux, Galaxy, deepTools)
+
+***
+
+# Why R ?
+* Standard software for data analysis, statistics, and visualization
+* free and community support
+* many packages available (for data I/O, manipulation, high-end: expression analysis)
+* good compromise between flexibility (programming) and box-solutions (packages)
+* suitable for very large dataset (filtering, merging)
+* interactive and scripting
+* not the best solution for everything (e.g. mapping)
+* frequent requirement during (bioinformatics) hiring
+
+***
+
+# Embrace the learning curve 
+
+*  steep (but rewarding)
+* First hurdles:
+  * it's a new language: vocabulary & grammar
+  * choices: many ways to say (to program) the same things
+  * more choices: many (redundant) packages
+  * computers are stubborn and stupid: they do not think along
+* More hurdles
+  * case sensitivity: $a \ne A$
+  * parameter sensitivity
+  * sofware dependencies
+
+***
+
+# Start Rstudio