A curated list of bioinformatics training material. All material is:
- In a GitHub or GitLab repository
- Free to use
- Written in markdown or similar
NOTE: This list of courses is selected only based on the above criteria. There are no checks on quality.
Is your (favourite) course not in there? Is a link dead? Did you find a typo? Any contribution to this list is highly appreciated 👍. Please have a look at CONTRIBUTING.md first.
- Scripting and languages
- Sequence data analysis
- Computational methods and pipelines
- Statistics and machine learning
- Reproducibility and data management
- Image analysis
- Other lists
- SIB First Steps with UNIX
- Carpentries The Unix Shell | website
- Carpentries Introduction to the Command Line for Genomics | website
- bioinformaticsworkbook.org Introduction to Unix | website
- Harvard Chan Bioinformatics Core Introduction to the command-line interface (shell) | website
- Ted Laderas Bash for bioinformatics | website
- SIB First Steps with Python in Life Sciences
- SIB Intermediate Python : "data analysis and representation" & "
harderfaster better stronger : optimizing python code" - Carpentries Programming with Python | website
- Harvard Chan Bioinformatics Core Introduction to Python | website
- Carpentries Interactive Data Visualizations in Python | website
- Jake van der Plas Python Data Science Handbook | website
- Jake van der Plas A Whirlwind Tour of Python | website
- Michigan State University Plants and Python | website
- VIB Gentle hands-on introduction to Python programming
- SIB First Steps with R in Life Sciences
- Carpentries R for Reproducible Scientific Analysis | website
- Harvard Chan Bioinformatics Core Introduction to R | website
- Harvard Chan Bioinformatics Core Introduction to R - Practical workshop | website
- DKFZ University of Heidelberg Basic R course | website
- CRG Introduction to R (2021) | website
- CRG Intermediate R: introduction to data wrangling with the Tidyverse (2021) | website
- NHS Rmarkdown: reproducible reporting | website
- Moderndive Statistical Inference via Data Science | website
- Rafael A. Irizarry Introduction to Data Science | website
- Bradley Boehmke Intro to R Bootcamp | website
- Julia Silge and David Robinson Text mining with R | website
- Rstudio R Markdown: The Definitive Guide | website
- Jennifer Bryan purrr tutorial | website
- Australian Biocommons Introduction to data analysis with R and Bioconductor | website
- rstudio::conf 2022 Graphic Design with ggplot2 | website
- rstudio::conf 2022 Building Production-Quality Shiny Applications | website
- rstudio::conf 2022 What They Forgot to Teach You About R | website
- rstudio::conf 2022 Getting Started with Quarto | website
- rstudio::conf 2022 Building tidy tools | website
- rstudio::conf 2022 Art from code | website
- rstudio::conf 2022 Introduction to the tidyverse | website
- rstudio::conf 2022 Getting Started with Shiny | website
- rstudio::conf 2022 Designing the Data Science Classroom | website
- Hadley Wickham Advanced R | website
- Nathaniel D. Philips YaRrr! The Pirate’s Guide to R | website
- Unversity of Manchester Data analysis using R | website
- Hadley Wickham and Garett Grolemund R for data science | website
- Oscar Baruffa Big book of R | website
- Norm Matloff fasteR
- Sean Davis Intro to R | website
- Colin Gillespie and Robin Lovelace Efficient R programming | website
- Chenxin Li Online R learning
- bioinformatics.ca Analysis using R 2021 | website
- bioinformatics.ca Introduction to R 2021 | website
- Carpentries The bioconductor project | website
- Rstudio eduction Data science box | website
- University of California, Irvine Introduction to Data Science | website
- University of Edinburgh Introduction to Data Science | website
- Duke University Introduction to Data Science | website
- Joachim Goedhart An introduction to data visualization protocols for wet lab scientists | website
- Ted Laderas R Bootcamp | website
- Ted Laderas A gRadual Introduction to Shiny | website
- Carpentries High dimensional statistics with R | website
- Melbourne Bioinformatics An Introduction to R for Biologists | website
- Colautti Lab R Crash Course | website
- Bruno Rodrigues Reproducible Analytical Pipelines - Master's of Data Science | website
- Openscapes Making shareable documents with Quarto | website
- UCSB-MEDS Creating quarto websites | websites
- UCSB-MEDS Customizing quarto websites | websites
- SIB NGS: Quality control, Alignment, Visualisation | website
- Harvard Chan Bioinformatics Core Accessing genomic reference and experimental sequencing data | website
- CRUK Workshop on Functional Genomics - summer school 2020 | website
- Carpentries Data Wrangling and Processing for Genomics | website
- Mike Love Introduction to Computational Biology | website
- bioinformatics.ca High Throughput Genomics Analysis | website
- St. Jude Children's Research Hospital Learn Genomics| website
- Melbourne Bioinformatics Bioinformatics Documentation | website
- Griffiths lab pmbio.org | website
- Mike Lee Happy Belly Bioinformatics | website
- James W. MacDonald Introduction to Bioconductor annotation resources | website
- Waldron lab CUNY Public data resources and Bioconductor | website
- Waldron lab CUNY Functional enrichment analysis of high-throughput omics data | website
- WEHI Gene-set enrichment analysis workshop | website
- Waldron lab CUNY Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment | website
- SIB Enrichment Analysis | website
- bioinformatics.ca Cancer Analysis 2021 | website
- bioinformatics.ca Infectious Disease Epidemiology Analysis 2021 | website
- bioinformatics.ca Pathway Network Analysis 2021 | website
- The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre Biomarker discovery from high throughput screening datasets | website
- James W. MacDonald Introduction to Bioconductor annotation resources | website
- Chloe Mirzayi Epidemiology for Bioinformaticians | website
- SIB Introduction to RNA-Seq: From quality control to pathway analysis | website
- Carpentries RNA-seq analysis with Bioconductor | website
- bioinformaticsworkbook.org RNA-Seq data Analysis | website
- bioinformaticsworkbook.org Differential Gene Expression analysis | website
- Harvard Chan Bioinformatics Core Introduction to bulk RNA-seq | website
- Harvard Chan Bioinformatics Core Differential Gene Expression Analysis | website
- CRUK CI Introduction to Bulk RNA-seq data analysis | website
- Stefano Mangiola A Tidy Transcriptomics introduction to RNA sequencing analyses | website
- WEHI Workshop: RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR | website
- EBI Bulk RNA-seq tutorial | website
- CRG RNAseq course 2019 | website
- Dan Beiting DIYtranscriptomics | website
- bioinformatics.ca RNA-seq Analysis 2021 | website
- Harvard Chan Bioinformatics Core Introduction to ChIP-seq using high performance computing | website
- CRUK CI Quantitiative analysis of ChiP-seq, ATAC-seq, and related DNA enrichment assays
- UMass MCCB Best practices for ATAC-seq QC and data analysis | website
- UMass Integrated ChIP-seq Data Analysis Workshop | website
- bioinformatics.ca Epigenomic Analysis 2021 | website
- SIB Single-cell Transcriptomics | website
- SIB NBIS/SciLifeLab Advanced topics in Single Cell Omics | website
- SIB Advanced topics in single-cell transcriptomics
- CRUK CI Introduction to single-cell RNA-seq data analysis | website
- NBIS Single cell RNA-seq analysis workshop | website
- MGC/BioSB Course - Single Cell Analysis
- Harvard Chan Bioinformatics Core Single-cell RNA-seq data analysis workshop | website
- WEHI Single cell RNA-seq analysis workshop | website
- Dana-Farber Cancer Institute Trajectory inference across conditions: differential expression and differential progression | website
- ELIXIR EXCELERATE Single RNA-seq data analysis with R | website
- EBI Single cell RNA-seq tutorial | website
- Wellcome Sanger Institute Analysis of single cell RNA-seq data | website
- Aedin Culhane basic scRNAseq workflow | website
- Martin Morgan introduction to Human Cell Atlas data retrieval and analysis in R / Bioconductor | webiste
- Tidy-transcriptomics workshops Tidy Transcriptomics For Single-Cell RNA Sequencing Analyses | website
- SIB NGS - Genome variant analysis | website
- bioinformaticsworkbook.org Variant Discovery | website
- WEHI A introduction to SNV analyses in whole genome sequencing | website
- Waldron lab CUNY Copy number variation analysis with Bioconductor | website
- Sateesh Peri Nextflow Tutorial - Variant Calling Edition | website
- bioinformaticsworkbook.org Introduction to Genome Assembly | website
- Katharina Hoff BRAKER-TSEBRA-Workshop
- Waldron lab CUNY Curated Metagenomic Analyses | website
- bioinformatics.ca Microbiome Analysis 2021 | website
- Matteo Calgaro An introduction to benchdamic | website
- SIB Docker and Singularity for reproducible research: getting started with containers | website
- Carpentries Reproducible Computational Environments Using Containers: Introduction to Docker | website
- Carpentries Reproducible computational environments using containers: Introduction to Singularity | website
- rOpenSci Labs R Docker tutorial | website
- Bioconductor Docker containers for Bioconductor | website
- Awesome workshop Docker/Singularity HATS@LPC | website
- CRG SIB Reproducible research and data analysis using Nextflow pipelines | website
- Carpentries Introduction to Bioinformatics workflows with Nextflow and nf-core | website
- CRG BovReg Nextflow training | website
- CRG Reproducible research and data analysis with Linux containers and Nextflow pipelines | website
- CRUK CI nextflow_september_2021
- Sateesh Peri Nextflow Tutorial - Variant Calling Edition | website
- CRG ELIXIR Containers and Workflow Pipelines for reproducible and automated data analysis | website
- Seqera labs Nextflow training | website
- VIB ELIXIR Nextflow Pipelines for reproducible and automated data analysis | website
- Snakemake Snakemake Tutorial | website
- Carpentries Snakemake for Bioinformatics | website
- Carpentries Getting Started with Snakemake | website
- Roswell Park Connecting Bioconductor to other bioinformatics tools using
Rcwl| website - INAB/CERTH Introduction to CWL and Docker | website
- Carpentries Introduction to High-Performance Computing | website
- NIH CFDE Introduction to Remote Computing | website
- Danielle Navarro Learning Statistics with R | website
- CRUK CI Introduction to Statistical Analysis | website
- CRUK CI Experimental design | website
- CRUK CI linear-models-r | website
- Aedin Culhane Dimension Reduction for Beginners: Hitchhiker’s Guide to Matrix Factorization and PCA | website
- SIB Statistics and Machine Learning (Python)
- Richard McElreath Statistical Rethinking (2022 Edition)
- SIB Advanced statistics: Statistical modelling | website
- SIB Learning statistics with R | website
- SIB Introduction to Bayesian statistics with R
- SIB Introduction to Statistics for Life Science - with python
- Carpentries Statistical thinking for public health | website
- SIB Introduction to Machine Learning (Python)
- Carpentries Introduction to Machine Learning with Scikit Learn | website
- Carpentries Introduction to Machine Learning in Python | website
- fastai Practical Deep Learning for Coders | website
- bioinformatics.ca Machine Learning 2021 | website
- Phillip Lippe UvA Deep Learning Tutorials | website
- INRIA Machine learning in Python with scikit-learn MOOC | website
- Harvard Chan Bioinformatics Core Tools for Reproducible Research | website
- Carpentries FAIR in (biological) practice | website
- Carpentries Introduction to Conda for (Data) Scientists | website
- FAIRplus FAIR Cookbook | website
- Carpentries Fair for leaders | website
- SIB Personalized Health informatics Group FAIR principles in practice for health data | website
- Carpentries From a Spreadsheet to a Database | website
- CRUK CI Managing your Research Data: Best practices in Research Data Management for Biological Sciences | website
- ELIXIR Europe RDMkit | website
- ELIXIR Belgium RDM guide | website
- ELIXIR Norway 2022-09-26 DMP-writing-workshop | website
- ELIXIR Norway FAIR Data Management in Life Sciences - June 2022 Course
- SIB Query SIB resources with SPARQL
- SIB Personalized Health Informatics Group SPHN Training material | website