See this page for help with obtaining teaching material from GitLab and GitHub.
Bio-IT Courses
Follow the links below to access materials for Bio-IT courses. You might also be interested in our list of useful cheat sheets.
Introduction to Python Programming
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf
Image Analysis with Python
Maintainer: Jonas Hartmann
homepage
Introduction to R Programming
Maintainer: Nicolas Descostes
homepage
Introduction to Linux Command Line
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf
Intermediate Linux Command Line
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf
Git Fundamentals
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf
Introduction to Regular Expressions
Maintainer: Renato Alves previously Toby Hodges
homepage | repository
Scientific Data Management
Maintainer: Renato Alves previously Toby Hodges
homepage
Snakemake Training
Snakemake Example
Maintainer: Christian Arnold
homepage
Snakemake Tutorial
Maintainer: Thomas Schwarzl
homepage
Cluster Training
Introduction to High Performance Computing at EMBL
Maintainer: Mike Smith
course repository
Hands-On with the New EMBL HPC Cluster
Maintainer: Jure Pečar
slides
jug @ EMBL
Maintainer: Renato Alves
slides | repository
Wrapping tools with merit
Maintainer: Markus Fritz/GBCS
slides
merit repository
Singularity Training
Introduction to Container Computing with Singularity
Maintainer: Josep Moscardó
course repository
CSDA Courses
Biostatistical Basics
Maintainer: Sarah Kaspar
course home page
Older CSDA course materials can be found at Bernd Klaus's homepage. They include:
- Introduction to R (using the tidyverse)
- Data handling and graphics with R (using the tidyverse)
- Exploratory data analysis and ggplot2
- Statistical methods for bioinformatics
- Hypothesis testing
- Differential expression analysis of RNA-Seq data with DESeq2
- Machine learning
- Analysis of high throughput microscopy data
CBNA Courses
Materials from courses taught by the Centre for Biomolecular Network Analysis are available via the CBNA pages. Courses include:
- Introduction to Network Biology
- Cytoscape (introduction & intermediate)
- Chromatin Signatures During Differentiation (EMBl course)
- Networks and Pathways (EMBL-EBI course)
- Integration of Transcriptome and Proteome (EMBL course)
- From Beginner to Intermediate in 3 Days Omicron Workshop on Network Biology (Jagiellonian University, Collegium Medicum)
- Intermediate Network Analysis - Automation and Scripting in Cytoscape and R iGraph
CBM Courses
Introduction to MATLAB
Maintainer: Eva Geissen
homepage
PreDoc Course
What is version control (with git)
Maintainer: Renato Alves
slides | repository
Introduction to Python
Maintainer: Renato Alves
slides | repository
Introduction to Python IO and plotting
Maintainer: Renato Alves
slides | repository