Bioinformatics training materials

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Below you'll find a curated list of bioinformatics training material. All material is:

• In a GitHub or GitLab repository (repositories in self-managed instances of GitLab are not supported anymore..)
• 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.

Contents

• Scripting and languages
  • Version control
  • Unix/Linux
  • Python
  • R
  • Quarto
  • Shiny
  • Julia
  • Data visualization
  • Java
  • GNU Make
  • MATLAB/Octave
  • SQL
  • C/C++
  • Rust
  • SPARQL
  • LaTeX
• Computational methods and pipelines
  • Containerization
  • Galaxy
  • High performance computing
  • Workflows
  • Image analysis
  • Cloud computing
• Omics analysis
  • Genomics
  • Next generation sequencing
  • Transcriptomics
  • RNA-seq
  • Single-cell sequencing
  • Variant analysis
  • ChIP-seq
  • Comparative genomics
  • Epigenetics
  • Genome annotation
  • Genome assembly
  • Metagenomics
  • Epidemiology
  • Microbiology
  • Multiomics
  • Spatial transcriptomics
  • Long read sequencing
  • Metabolomics
  • Proteomics
  • Pathways and Networks
• Reproducibility and data management
  • Data management
  • FAIR data
  • Reproducibility
• Statistics and machine learning
  • Data science
  • Statistics
  • Machine learning
  • Artificial intelligence
• Others
  • General

Scripting and languages

Version control

• Software Carpentry swcarpentry/git-novice | website
• BioinfGuru BioinfGuru/gitTutorial
• Kottans kottans/git-course | website
• Gerard Capes gcapes/git-course | website
• carpentries-incubator carpentries-incubator/gitlab-novice | website
• Data Carpentry datacarpentry/rr-version-control | website
• VIB Technologies: Training material and software projects vibbits/introduction-github
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-versioning-dm-practices | website
• Sergio Martínez Cuesta semacu/20190927_IntroductionGithub_HDRUK
• Sergio Martínez Cuesta semacu/20181003_Intro_git_GitHub
• Sergio Martínez Cuesta semacu/20171024_GitHub_Chemistry_Cambridge
• jhudsl jhudsl/Adv_Reproducibility_in_Cancer_Informatics | website
• posit::conf(2024) posit-conf-2024/dev-ops

Unix/Linux

• Data Carpentry datacarpentry/shell-genomics | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Intro-to-shell-flipped | website
• Ted Laderas laderast/bash_for_bioinformatics | website
• SIB Swiss Institute of Bioinformatics sib-swiss/unix-first-steps-training
• Software Carpentry swcarpentry/shell-novice | website
• Sundeep Agarwal learnbyexample/cli_text_processing_coreutils | website
• Sundeep Agarwal learnbyexample/cli-computing | website
• Sundeep Agarwal learnbyexample/learn_gnuawk | website
• Sundeep Agarwal learnbyexample/learn_gnused | website
• Sundeep Agarwal learnbyexample/learn_gnugrep_ripgrep | website
• slackermedia slackermedia/bashcrawl
• carpentries-incubator carpentries-incubator/shell-extras | website
• The Carpentries Lab carpentries-lab/metagenomics-shell | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-September-Introduction-to-the-Command-Line-for-Bioinformatics
• Cloud-SPAN Cloud-SPAN/prenomics00-intro | website
• Sergio Martínez Cuesta semacu/20180726_TrainMalta_Unix_R
• Bobby Iliev bobbyiliev/introduction-to-bash-scripting | website
• Firas Zemzem Zemzemfiras1/Mastering_Linux_Tutorials
• Jeroen Janssens jeroenjanssens/data-science-at-the-command-line | website

Python

• carpentries-incubator carpentries-incubator/introduction-to-conda-for-data-scientists | website
• carpentries-incubator carpentries-incubator/python-interactive-data-visualizations | website
• Jake Vanderplas jakevdp/PythonDataScienceHandbook | website
• Jake Vanderplas jakevdp/WhirlwindTourOfPython
• Plants&Python PlantsAndPython/PlantsAndPython
• SIB Swiss Institute of Bioinformatics sib-swiss/first-steps-with-python-training
• SIB Swiss Institute of Bioinformatics sib-swiss/intermediate-python-training
• Software Carpentry swcarpentry/python-novice-inflammation | website
• VIB Technologies: Training material and software projects vibbits/gentle-hands-on-python
• Talk Python talkpython/python-for-absolute-beginners-course | website
• Sundeep Agarwal learnbyexample/py_regular_expressions | website
• Sundeep Agarwal learnbyexample/100_page_python_intro | website
• Alex Hall alexmojaki/futurecoder | website
• Guillaume Gautier guilgautier/sdia-python
• cambiotraining cambiotraining/python-data-science
• carpentries-incubator carpentries-incubator/python-text-analysis | website
• carpentries-incubator carpentries-incubator/python_packaging | website
• carpentries-incubator carpentries-incubator/python-testing | website
• carpentries-incubator carpentries-incubator/python-intermediate-development | website
• carpentries-incubator carpentries-incubator/python-packaging-publishing | website
• carpentries-incubator carpentries-incubator/lesson-parallel-python | website
• Data Carpentry datacarpentry/python-ecology-lesson | website
• The Algorithms TheAlgorithms/Python | website
• Oleksii Trekhleb trekhleb/learn-python
• João Ventura joaoventura/full-speed-python
• Sebastian Raschka rasbt/python_reference
• Jeffrey Hu zhiwehu/Python-programming-exercises
• LiaBooks ... by LiaScript LiaBooks/How-To-Code-in-Python-3 | website
• LiaPlayground LiaPlayground/PythonProgramming
• Valentin Danchev valdanchev/reproducible-data-science-python
• Girls Who Code at U-M DCMB GWC-DCMB/GWC-DCMB | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-July-Introduction-To-Python-For-Bioinformatics
• The Gulbenkian Training Programme in Bioinformatics GTPB/PPB18 | website
• Swaroop CH swaroopch/byte-of-python | website
• S.Lott slott56/building-skills-oo-design-book | website
• Real Python realpython/python-guide | website
• OpenTechSchool OpenTechSchool/python-beginners | website
• Ankit Mahato animator/learn-python | website
• Sundeep Agarwal learnbyexample/practice_python_projects | website
• SoftUni SoftUni/Programming-Basics-Book-Python-EN | website
• Akuli Akuli/python-tutorial
• Charles Severance csev/py4e | website
• Kushal Das kushaldas/pym
• Greg Malcolm gregmalcolm/python_koans
• BioINForm bioinform-org/bioinforming-hs
• Daniel Chen chendaniely/positconf2023-academy_python
• Rami Krispin RamiKrispin/vscode-python
• Wes McKinney wesm/pydata-book
• Lino Galiana linogaliana/python-datascientist | website
• Kevin Heavey kevinheavey/modern-polars | website
• Python Packages py-pkgs/py-pkgs | website
• bioinfo-prog bioinfo-prog/cours-python | website
• R. Burke Squires burkesquires/python_biologist
• Sergio Martínez Cuesta semacu/data-science-python
• MolSSI Education MolSSI-Education/python_scripting_cms | website
• Jean de Dieu Nyandwi Nyandwi/PythonBasics

R

• Bruno Rodrigues b-rodrigues/rap4mads | website
• BHKLAB bhklab/bioc2020workshop | website
• Bioconductor Bioconductor/bioconductor_docker | website
• Biocore@CRG biocorecrg/CRG_R_tidyverse_2021
• Biocore@CRG biocorecrg/CRG_RIntroduction_2021
• Canadian Bioinformatics Workshops bioinformatics-ca/AUR_2021
• Canadian Bioinformatics Workshops bioinformatics-ca/INR_2021
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/linear-models-r | website
• Bradley Boehmke bradleyboehmke/Intro-to-R-Bootcamp
• carpentries-incubator carpentries-incubator/bioc-project | website
• carpentries-incubator carpentries-incubator/high-dimensional-stats-r | website
• Colautti Lab ColauttiLab/RCrashCourse_Book
• Computational Cancer Biology and Epigenomics CompEpigen/BasicR | website
• Colin Gillespie csgillespie/efficientR | website
• C. Li cxli233/Online_R_learning
• Davis Laboratory DavisLaboratory/GenesetAnalysisWorkflow | website
• David Robinson dgrtwo/tidy-text-mining | website
• Danielle Navarro djnavarro/rbook | website
• Duke Department of Statistical Science DukeStatSci/introds | website
• Hadley Wickham hadley/adv-r | website
• Hadley Wickham hadley/r4ds | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Intro-to-R-flipped | website
• ICS 80 - Introduction to Data Science ics80-fa21/website | website
• Introduction to Data Science - 2020 - Semester 1 ids-s1-20/website | website
• Jennifer (Jenny) Bryan jennybc/purrr-tutorial | website
• James W. MacDonald jmacdon/Bioc2020Anno
• James W. MacDonald jmacdon/Bioc2022Anno
• Joachim Goedhart JoachimGoedhart/DataViz-protocols | website
• Jemma Stachelek jsta/r-docker-tutorial | website
• Tom Mock jthomasmock/rmd-nhs | website
• Ted Laderas laderast/gradual_shiny | website
• Ted Laderas laderast/RBootcamp | website
• Qian Liu Liubuntu/Bioc2020RCWL
• Norm Matloff matloff/fasteR
• Melbourne Bioinformatics melbournebioinformatics/r-intro-biologists
• ModernDive moderndive/ModernDive_book | website
• Nathaniel Phillips ndphillips/ThePiratesGuideToR | website
• Openscapes Openscapes/quarto-website-tutorial | website
• Oscar Baruffa oscarbaruffa/BigBookofR | website
• Rafael A Irizarry rafalab/dsbook
• rstudio::conf(2022) rstudio-conf-2022/art-from-code | website
• rstudio::conf(2022) rstudio-conf-2022/build-tidy-tools | website
• rstudio::conf(2022) rstudio-conf-2022/get-started-quarto | website
• rstudio::conf(2022) rstudio-conf-2022/get-started-shiny | website
• rstudio::conf(2022) rstudio-conf-2022/ggplot2-graphic-design | website
• rstudio::conf(2022) rstudio-conf-2022/intro-to-tidyverse | website
• rstudio::conf(2022) rstudio-conf-2022/shiny-prod-apps | website
• rstudio::conf(2022) rstudio-conf-2022/teach-ds | website
• rstudio::conf(2022) rstudio-conf-2022/wtf-rstats
• RStudio Education tidyverse/datascience-box | website
• RStudio rstudio/rmarkdown-book | website
• Saskia SaskiaFreytag/biocommons-r-intro | website
• Sean Davis seandavi/ITR | website
• SIB Swiss Institute of Bioinformatics sib-swiss/enrichment-analysis-training | website
• SIB Swiss Institute of Bioinformatics sib-swiss/first-steps-with-R-training
• Software Carpentry swcarpentry/r-novice-gapminder | website
• Research IT, University of Manchester, UK UoMResearchIT/r-tidyverse-intro | website
• Waldron Lab at the CUNY SPH waldronlab/enrichOmics
• Jennifer (Jenny) Bryan jennybc/happy-git-with-r | website
• Bioinformatics, Rockefeller University RockefellerUniversity/Bioconductor_Introduction | website
• Bioinformatics, Rockefeller University RockefellerUniversity/Intro_To_R_1Day | website
• Bioinformatics, Rockefeller University RockefellerUniversity/RU_reproducibleR | website
• Bioinformatics, Rockefeller University RockefellerUniversity/RU_tidyverse_core | website
• Bioinformatics, Rockefeller University RockefellerUniversity/RU_GenomicVariants
• Hadley Wickham hadley/r-pkgs | website
• Hadley Wickham hadley/mastering-shiny | website
• Dirk Eddelbuettel eddelbuettel/gsir-te
• carpentries-incubator carpentries-incubator/bioc-intro | website
• Will Landau wlandau/targets-tutorial | website
• R Programming @ University of Cincinnati uc-r/Advanced-R
• R Programming @ University of Cincinnati uc-r/Intro-R
• R Programming @ University of Cincinnati uc-r/Intermediate-R
• RStudio Education rstudio-education/advanced-shiny-az | website
• RStudio rstudio/learnr | website
• dcruvolo davidruvolo51/shinyAppTutorials | website
• Max Planck Institute of Immunobiology and Epigenetics maxplanck-ie/Rintro
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/r-basics
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-data-visualization-r
• carpentries-incubator carpentries-incubator/lc-litsearchr | website
• carpentries-incubator carpentries-incubator/R-ecology-lesson | website
• carpentries-incubator carpentries-incubator/R-ecology-lesson-intermediate | website
• carpentries-incubator carpentries-incubator/open-science-with-r | website
• carpentries-incubator carpentries-incubator/reproducible-publications-quarto | website
• Data Carpentry datacarpentry/R-ecology-lesson | website
• Data Carpentry datacarpentry/genomics-r-intro | website
• Data Carpentry datacarpentry/rr-automation | website
• Data Carpentry datacarpentry/rr-literate-programming
• RStudio Education rstudio-education/stat545 | website
• nullranges tidyomics/tidy-ranges-tutorial | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-epigenomics-RTDs | website
• Library Data Services UNC-Libraries-data/R-Open-Labs | website
• Greg Wilson gvwilson/tidynomicon | website
• Vince Carey vjcitn/BiocPyInterop | website
• Bioinformatics, Rockefeller University RockefellerUniversity/RU_VisualizingGenomicsData
• genomicsclass genomicsclass/book | website
• Kristyna Kupkova kkupkova/GenomicDistributionsBioC2022
• Workflow Languages in R rworkflow/RcwlWorkshop | website
• tidyomics tidyomics/tidyomicsWorkshopBioc2023 | website
• Surgical Informatics SurgicalInformatics/healthyr_book | website
• Trevor French TrevorFrench/R-for-Data-Analysis | website
• UM Carpentries UMCarpentries/intro-curriculum-r | website
• rostools rostools/r-cubed-intro | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-rstudio-intro-dm-practices | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-r-intro-dm-practices | website
• bioinformatics.ca bioinformaticsdotca/AUR_2023
• Computational Biology and Bioinformatics at UCLouvain UCLouvain-CBIO/WSBIM1207 | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-June-Introduction-to-R-for-Bioinformatics
• Institut Français de Bioinformatique (IFB) IFB-ElixirFr/IFB_Shiny_training | website
• bioinformatics.ca bioinformaticsdotca/INR_2023
• ELIXIR Estonia ELIXIREstonia/2023-10-24-R-basic | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/ABSTAT18 | website
• Hugo Tavares tavareshugo/2018-06-28-cambridge | website
• Sergio Martínez Cuesta semacu/20180531_DataVisualisationRggplot2_Wolfson_Cambridge
• Data Carpentry datacarpentry/ecology-workshop | website
• Jacques van Helden jvanheld/stats_avec_RStudio_EBA | website
• Paul Roback proback/BeyondMLR
• Data Challenge Lab Open Content dcl-docs/prog | website
• G. Jay Kerns gjkerns/IPSUR | website
• Roger D. Peng rdpeng/rprogdatascience
• Marek Gagolewski gagolews/deepr | website
• bougioukas bougioukas/practical_stats_med-r
• TaniaW taniawyss/flow-cytometry-analysis-with-R | website
• Roger D. Peng rdpeng/exdata
• Rafael A Irizarry rafalab/dsbook-part-1
• Rafael A Irizarry rafalab/dsbook-part-2
• Causal Inference in R r-causal/causal-inference-in-R | website
• posit-conf-2023 posit-conf-2023/r-intro | website
• posit-conf-2023 posit-conf-2023/forecasting | website
• tidymodels tidymodels/workshops | website
• posit-conf-2023 posit-conf-2023/pkg-dev-masterclass
• posit-conf-2023 posit-conf-2023/pkg-dev | website
• What They Forgot to Teach You About R rstats-wtf/what-they-forgot | website
• posit-conf-2023 posit-conf-2023/arrow | website
• posit-conf-2023 posit-conf-2023/dataviz-storytelling | website
• posit-conf-2023 posit-conf-2023/ds-workflows-r | website
• posit-conf-2023 posit-conf-2023/vetiver | website
• posit-conf-2023 posit-conf-2023/programming-r | website
• posit-conf-2023 posit-conf-2023/teach-ds-masterclass | website
• posit-conf-2023 posit-conf-2023/dataviz-ggplot2 | website
• posit-conf-2023 posit-conf-2023/creative-coding
• Rami Krispin RamiKrispin/vscode-r
• Winston Chang wch/rgcookbook | website
• RStudio rstudio/rmarkdown-cookbook | website
• RStudio rstudio/bookdown | website
• RStudio Education rstudio-education/hopr
• swirl development team swirldev/swirl | website
• JD Long CerebralMastication/R-Cookbook
• r-spark r-spark/the-r-in-spark | website
• R for the Rest of Us rfortherestofus/book
• Michael Teske mictes/Shiny_Tutorial | website
• jjallaire jjallaire/hopr
• Rohan Alexander RohanAlexander/telling_stories | website
• Leonardo Collado-Torres lcolladotor/cshl_rstats_genome_scale_2024 | website
• Sophie Lee sophie-a-lee/Introduction_R_Tidyverse_course | website
• Sophie Lee sophie-a-lee/intro-rstudio-mhclg | website
• Stephen Turner stephenturner/workshops | website
• Fred Hutch Data Science Lab fhdsl/Tools_for_Reproducible_Workflows_in_R | website
• Aditya Dahiya Aditya-Dahiya/ggplot2book3e
• posit::conf(2024) posit-conf-2024/arrow | website
• posit::conf(2024) posit-conf-2024/ds-workflows-r | website
• posit::conf(2024) posit-conf-2024/databases | website
• posit::conf(2024) posit-conf-2024/pharmaverse | website
• posit::conf(2024) posit-conf-2024/programming-r | website
• Northwestern IT Research Computing and Data Services nuitrcs/R-intro-tidyverse-2024
• posit::conf(2024) posit-conf-2024/tables
• posit::conf(2024) posit-conf-2024/pkg-dev
• posit::conf(2024) posit-conf-2024/r-in-production
• posit::conf(2024) posit-conf-2024/databricks | website
• posit::conf(2024) posit-conf-2024/wtf

Quarto

• Master of Environmental Data Science (MEDS) program UCSB-MEDS/customizing-quarto-websites | website
• Master of Environmental Data Science (MEDS) program UCSB-MEDS/creating-quarto-websites | website
• posit-conf-2023 posit-conf-2023/quarto-r | website
• Hamel Husain hamelsmu/posit-python-quarto | website
• Isabella Velásquez ivelasq/2024-01-23_getting-started-with-report-writing-using-quarto | website
• Julien Roux julien-roux/SIB_days_2024_workshop_EDI
• posit::conf(2024) posit-conf-2024/quarto-dashboards | website
• posit::conf(2024) posit-conf-2024/quarto-websites | website

Shiny

• Martin J Frigaard mjfrigaard/shinypak | website
• Rami Krispin RamiKrispin/shinylive-r | website
• posit-dev posit-dev/py-shiny-workshop | website
• posit-conf-2023 posit-conf-2023/shiny-r-intro | website
• posit-conf-2023 posit-conf-2023/shiny-r-ui | website
• posit-conf-2023 posit-conf-2023/shiny-r-dashboard | website
• posit-conf-2023 posit-conf-2023/shiny-r-prod | website
• ThinkR ThinkR-open/engineering-shiny-book | website
• Ted Laderas laderast/shinyowl | website
• posit-dev posit-dev/intro-to-shiny-for-python | website
• posit::conf(2024) posit-conf-2024/shiny-r-intro | website
• posit::conf(2024) posit-conf-2024/level-up-shiny | website

Julia

• Antonello Lobianco sylvaticus/juliatutorial
• JuliaAcademy JuliaAcademy/JuliaTutorials | website
• JuliaAcademy JuliaAcademy/DataScience | website
• JuliaAcademy JuliaAcademy/Introduction-to-Julia | website
• JuliaAcademy JuliaAcademy/JuliaProgrammingForNervousBeginners | website
• JuliaAcademy JuliaAcademy/DataFrames
• JuliaAcademy JuliaAcademy/Foundations-of-Machine-Learning | website
• carpentries-incubator carpentries-incubator/julia-novice | website
• Antonello Lobianco sylvaticus/SPMLJ | website
• Ben Lauwens BenLauwens/ThinkJulia.jl
• Claudia Solis-Lemus crsl4/julia-workshop | website

Data visualization

• Bioinformatics, Rockefeller University RockefellerUniversity/IGV_course | website
• Hadley Wickham hadley/ggplot2-book | website
• Christian Burkhart ch-bu/ggplot2-fundamentals | website
• carpentries-incubator carpentries-incubator/intro-data-viz | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/publication_perfect | website
• C. Li cxli233/FriendsDontLetFriends
• Claus Wilke clauswilke/dataviz | website
• Hands-On Data Visualization HandsOnDataViz/book | website
• Carson Sievert cpsievert/plotly_book | website
• Colin Diesh cmdcolin/awesome-genome-visualization | website
• UW Interactive Data Lab uwdata/visualization-curriculum | website
• Fred Hutch Data Science Lab fhdsl/better_plots | website
• Kyran Dale Kyrand/dataviz-with-python-and-js-ed-2

Java

• BioJava biojava/biojava-tutorial | website

GNU Make

• Software Carpentry swcarpentry/make-novice | website
• Chase Lambert theicfire/makefiletutorial | website

MATLAB/Octave

• Software Carpentry swcarpentry/matlab-novice-inflammation | website

SQL

• Data Carpentry datacarpentry/sql-ecology-lesson | website

C/C++

• LiaBooks ... by LiaScript LiaBooks/C-Programming | website

Rust

• Google google/comprehensive-rust | website
• The Rust Programming Language rust-lang/rustlings | website

SPARQL

• SIB Swiss Institute of Bioinformatics sib-swiss/sparql-training
• BiGCaT, Department of Translational Genomics BiGCAT-UM/SPARQLTutorialBioSB2019
• SIB Swiss Institute of Bioinformatics sib-swiss/SPARQL_course

LaTeX

• Fred Hutch Data Science Lab fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles | website

Computational methods and pipelines

Containerization

• awesome-workshop awesome-workshop/docker-singularity-hats | website
• carpentries-incubator carpentries-incubator/docker-introduction | website
• carpentries-incubator carpentries-incubator/singularity-introduction | website
• SIB Swiss Institute of Bioinformatics sib-swiss/containers-introduction-training | website
• PerMedCoE PerMedCoE/mpi-in-container
• Rami Krispin RamiKrispin/Introduction-to-Docker

Galaxy

• Erasmus Medical Center ErasmusMC-Bioinformatics/galaxy-courses
• Galaxy Project galaxyproject/training-material | website

High performance computing

• carpentries-incubator carpentries-incubator/hpc-intro | website
• ngs-docs ngs-docs/2021-august-remote-computing | website
• cambiotraining cambiotraining/hpc-intro | website
• carpentries-incubator carpentries-incubator/lesson-gpu-programming | website
• PerMedCoE PerMedCoE/cluster-tutorial
• George G. Vega Yon gvegayon/appliedhpcr
• jhudsl jhudsl/Computing_for_Cancer_Informatics | website

Workflows

• Biocore@CRG biocorecrg/CoursesCRG_Containers_Nextflow_May_2022 | website
• Biocore@CRG biocorecrg/ELIXIR_containers_nextflow | website
• Biocore@CRG biocorecrg/SIB_course_nextflow_Nov_2021 | website
• Biodata Analysis Group BiodataAnalysisGroup/intro-to-cwl-docker | website
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/nextflow_september_2021
• BovReg BovReg/nf-workshop20
• carpentries-incubator carpentries-incubator/snakemake-novice-bioinformatics | website
• carpentries-incubator carpentries-incubator/workflows-nextflow | website
• carpentries-incubator carpentries-incubator/workflows-snakemake | website
• Sateesh_Peri sateeshperi/nextflow_varcal | website
• Seqera nextflow-io/training | website
• VIB Technologies: Training material and software projects vibbits/nextflow-workshop
• SIB Swiss Institute of Bioinformatics sib-swiss/containers-snakemake-training | website
• carpentries-incubator carpentries-incubator/cwl-novice-tutorial | website
• Romain Feron RomainFeron/workshop-snakemake-sibdays2022
• Dockstore dockstore/bcc2020-training
• Fred Hutch Data Science Lab fhdsl/GitHub_Automation_for_Scientists | website

Image analysis

• Andrew Jahn andrewjahn/AndysBrainBook
• carpentries-incubator carpentries-incubator/SDC-BIDS-fMRI | website
• carpentries-incubator carpentries-incubator/SDC-BIDS-IntroMRI | website
• carpentries-incubator carpentries-incubator/SDC-BIDS-sMRI | website
• carpentries-incubator carpentries-incubator/SDC-BIDS-dMRI | website
• Data Carpentry datacarpentry/image-processing | website
• Dominic Waithe dwaithe/model-training
• NEUBIAS NEUBIAS/training-resources | website
• napari napari/napari-workshop-template | website
• Kyle I S Harrington kephale/napari-workshop-mandm-2023
• Chan Zuckerberg Initiative chanzuckerberg/napari-segmentation-workshop | website

Cloud computing

• Data Carpentry datacarpentry/cloud-genomics | website
• AWS Samples aws-samples/aws-hpc-tutorials | website
• Eija Korpelainen ekorpela/cloud-vm-workshop
• Lynn Langit lynnlangit/gcp-for-bioinformatics | website

Omics analysis

Genomics

• Canadian Bioinformatics Workshops bioinformatics-ca/CAN_2021
• Canadian Bioinformatics Workshops bioinformatics-ca/HTG_2021
• Papenfuss Lab PapenfussLab/IntroductionToGenomicsWorkshop
• Computational Metagenomics metagenomics/denbi-nanopore-training
• Computational Genomics with R compgenomr/book | website
• Wellcome Connecting Science WCSCourses/SARS-COV-2_B4B | website
• Functional Genomics Laboratory Functional-Genomics-Lab/Applied-Genomics | website
• cambiotraining cambiotraining/sars-cov-2-genomics | website
• Data Carpentry datacarpentry/genomics-workshop | website
• Data Carpentry datacarpentry/organization-genomics | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/ELB19F | website
• The McDonnell Genome Institute genome/bfx-workshop
• rapidspeciation rapidspeciation/biodiversity_genomics_course
• Applied Genomics Applied-Genomics-UTD/docs
• Fred Hutch Data Science Lab fhdsl/Choosing_Genomics_Tools | website

Next generation sequencing

• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/cruk-summer-school-2020 | website
• Data Carpentry datacarpentry/wrangling-genomics | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Accessing_public_genomic_data | website
• SIB Swiss Institute of Bioinformatics sib-swiss/NGS-introduction-training | website
• SIB Swiss Institute of Bioinformatics sib-swiss/NGS-variants-training | website
• Waldron Lab at the CUNY SPH waldronlab/CNVWorkshop | website
• The Griffith Lab griffithlab/pmbio.org | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-ngsintro | website
• Institut Français de Bioinformatique (IFB) IFB-ElixirFr/EBAII | website
• Cloud-SPAN Cloud-SPAN/00genomics | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-ngsintro | website

Transcriptomics

• Biocore@CRG biocorecrg/RNAseq_course_2019 | website
• Canadian Bioinformatics Workshops bioinformatics-ca/RNA_2021
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/Bulk_RNASeq_Course_Nov21 | website
• carpentries-incubator carpentries-incubator/bioc-rnaseq | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/DGE_workshop_salmon_online | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Intro-to-rnaseq-hpc-salmon-flipped | website
• SIB Swiss Institute of Bioinformatics sib-swiss/RNAseq-introduction-training | website
• Stefano Mangiola stemangiola/bioc_2020_tidytranscriptomics | website
• Tidy-transcriptomics workshops tidytranscriptomics-workshops/bioc2022_tidytranscriptomics | website
• Xueyi Dong XueyiDong/RNAseq123workshop
• Amarinder Singh Thind amarinderthind/RNA-seq-tutorial-for-gene-differential-expression-analysis
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/Bulk_RNASeq_Course_March23 | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-RNAseq | website
• Health Data Science Sandbox hds-sandbox/bulk_RNAseq_course | website
• Computational Biology and Bioinformatics at UCLouvain UCLouvain-CBIO/WSBIM2122 | website
• Saez Lab saezlab/transcriptutorial | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/ADER19F | website
• Khushbu Patel kpatel427/YouTubeTutorials

RNA-seq

• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/BBS230B_2023 | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/rnaseq-cb321
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/RNA-seq-CB321qc_2022
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/rnaseq_overview
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-June-RNA-Seq-Analysis
• bioinformatics.ca bioinformaticsdotca/RNA_2023
• bioinformatics.ca bioinformaticsdotca/PNA_2023
• The Griffith Lab griffithlab/rnabio.org | website

Single-cell sequencing

• Aedin Culhane aedin/scRNAseqBasicWorkflow
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/UnivCambridge_ScRnaSeq_Nov2021 | website
• fmicompbio fmicompbio/adv_scrnaseq_2020
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/scRNA-seq_online | website
• Kelly Street kstreet13/bioc2020trajectories | website
• Leiden Computational Biology Center LeidenCBC/MGC-BioSB-SingleCellAnalysis2021
• Martin Morgan mtmorgan/HCABiocTraining | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/excelerate-scRNAseq | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/single-cell_sib_scilifelab_2021
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-scRNAseq | website
• SIB Swiss Institute of Bioinformatics sib-swiss/single-cell-training | website
• Yunshun Chen yunshun/SingleCellWorkshop
• Cellular Genetics Informatics cellgeni/scRNA.seq.course | website
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/SingleCell_RNASeq_Jan23 | website
• OSCA Source Code Management OSCA-source/OSCA | website
• carpentries-incubator carpentries-incubator/scrna-seq-analysis | website
• Bioconductor Bioconductor/ISMB.OSCA | website
• Theis Lab theislab/single-cell-best-practices | website
• Health Data Science Sandbox hds-sandbox/scRNASeq_course | website
• Broad Institute broadinstitute/2020_scWorkshop | website
• Rhonda Bacher rhondabacher/ISMB2019_SingleCellTutorial
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-December-Single-Cell-RNA-Seq-Analysis
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-June-Single-Cell-RNA-Seq-Analysis
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2023-June-Advanced-Topics-in-Single-Cell-RNA-Seq-VDJ
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Advanced_Single_Cell_RNA_Seq
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2022-July-Advanced-Topics-in-Single-Cell-RNA-Seq-ATAC
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2021-August-Advanced-Topics-in-Single-Cell-RNA-Seq-Trajectory-and-Velocity
• bioinformatics.ca bioinformaticsdotca/scRNA_2023
• Theis Lab theislab/single-cell-tutorial
• PAIR code PAIR-code/understanding-umap | website
• material-share material-share/material-share-single-cell-boot-camp
• scverse scverse/scverse-tutorials | website
• CDSB ComunidadBioInfo/cdsb2021_scRNAseq | website
• Leiden Computational Biology Center LeidenCBC/MGC-BioSB-SingleCellAnalysis2022
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/SingleCell_RNASeq_May23 | website
• Alex's Lemonade Stand Foundation AlexsLemonade/2023-june-training
• Alex's Lemonade Stand Foundation AlexsLemonade/2023-march-training

Variant analysis

• Andries Marees MareesAT/GWA_tutorial
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/variant_analysis | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-pgip | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Variant_Analysis_Workshop
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2021-July-Genome-Wide-Association-Studies
• Nina Overgaard Therkildsen nt246/lcwgs-guide-tutorial
• Dipannita Ghosh digo4/Clinical-Genomics

ChIP-seq

• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/Quantitative-ChIPseq-Workshop
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Intro-to-ChIPseq | website
• hukai916 hukai916/IntegratedChIPseqWorkshop
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Intro-to-ChIPseq-flipped | website
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Peak_analysis_workshop
• Denis Puthier dputhier/EBA_2015_ChIP-Seq

Comparative genomics

• Steven M. Van Belleghem StevenVB12/stevenvb12.github.io
• The Gulbenkian Training Programme in Bioinformatics GTPB/CPANG19 | website

Epigenetics

• Haibo Liu haibol2016/ATACseqQCWorkshop
• bioinformatics.ca bioinformaticsdotca/EPI_2023
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Epigenetics_Workshop
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-epigenomics-RTDs | website

Genome annotation

• Katharina Hoff KatharinaHoff/BRAKER-TSEBRA-Workshop
• Katharina Hoff KatharinaHoff/BRAKER-TSEBRA-Workshop

Genome assembly

• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Genome_Assembly_Workshop
• ebp-nor ebp-nor/genome-assembly-workshop-2023

Metagenomics

• Canadian Bioinformatics Workshops bioinformatics-ca/MIC_2021
• Matteo Calgaro mcalgaro93/benchdamicWorkshop
• Waldron Lab at the CUNY SPH waldronlab/curatedMetagenomicDataAnalyses | website
• The Carpentries Lab carpentries-lab/metagenomics-workshop | website
• The Carpentries Lab carpentries-lab/metagenomics-organization | website
• The Carpentries Lab carpentries-lab/metagenomics-analysis | website
• The Carpentries Lab carpentries-lab/metagenomics-R | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2021-May-Microbial-Community-Analysis
• bioinformatics.ca bioinformaticsdotca/MIC_2023
• bioinformatics.ca bioinformaticsdotca/MIC_2022
• bioinformatics.ca bioinformaticsdotca/AMB_2024

Epidemiology

• Canadian Bioinformatics Workshops bioinformatics-ca/EPI_2021
• Canadian Bioinformatics Workshops bioinformatics-ca/IDE_2021
• Chloe Mirzayi cmirzayi/EpiForBioWorkshop2020 | website
• bioinformatics.ca bioinformaticsdotca/IDE_2023
• bioinformatics.ca bioinformaticsdotca/IDE_2024
• Alli Black alliblk/genepi-book | website

Microbiology

• bioinformatics.ca bioinformaticsdotca/BMB_2024

Multiomics

• Waldron Lab at the CUNY SPH waldronlab/MultiAssayWorkshop | website
• SIB Swiss Institute of Bioinformatics sib-swiss/multiomics-data-analysis-and-integration-training

Spatial transcriptomics

• Davis Laboratory DavisLaboratory/GeoMXAnalysisWorkflow | website
• dario righelli drighelli/SpatialExperiment_Bioc2021
• Integrative Computational Biology and Multiomics Research Group ncl-icbam/ismb-tutorial-2023
• Sydney Precision Data Science Centre SydneyBioX/StatialBioc2023 | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2022-December-Spatial-Transcriptomics
• Lukas Weber lmweber/BestPracticesST | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-spatial
• SIB Swiss Institute of Bioinformatics sib-swiss/spatial-transcriptomics-training | website

Long read sequencing

• SIB Swiss Institute of Bioinformatics sib-swiss/NGS-longreads-training | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2021-August-Iso-Seq
• Ryan Wick rrwick/Perfect-bacterial-genome-tutorial
• Tim Kahlke timkahlke/LongRead_tutorials

Metabolomics

• bioinformatics.ca bioinformaticsdotca/MET_2023

Proteomics

• Computational Biology and Bioinformatics at UCLouvain UCLouvain-CBIO/LSTAT2340 | website
• Health Data Science Sandbox hds-sandbox/proteomics-sandbox | website
• statOmics statOmics/PDA
• The Gulbenkian Training Programme in Bioinformatics GTPB/IBIP19 | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/PDA19 | website
• PickyBinders PickyBinders/geometric-learning-protein-structures-course

Pathways and Networks

• Canadian Bioinformatics Workshops bioinformatics-ca/PNA_2021
• Susan Coort/tutorial-network-data
• LaurenDupuis LaurenDupuis/EJP-RD_Helis_Academy

Reproducibility and data management

Data management

• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/Managing-your-research-data | website
• carpentries-incubator carpentries-incubator/capstone-novice-spreadsheet-biblio | website
• ELIXIR Belgium ELIXIR-Belgium/rdm-guide | website
• ELIXIR Europe elixir-europe/rdmkit | website
• ELIXIR-Norway Training ELIXIR-Norway-Training/DMP-writing-workshop | website
• OpenSciency opensciency/sprint-content | website
• SIB Swiss Institute of Bioinformatics sib-swiss/ena-seqdata-training | website
• VIB Technologies: Training material and software projects vibbits/rdm-introductory-course
• Utrecht University UtrechtUniversity/dataprivacyhandbook | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-dmp-dm-practices | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-data-publication-dm-practices | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-metadata-dm-practices | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-organising-data-dm-practices | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-open-science-dm-practices | website
• Health Data Science Sandbox hds-sandbox/RDM_biodata_course | website
• SIB Swiss Institute of Bioinformatics sib-swiss/Introduction-FAIR-RDM-DMP | website
• BioData.pt BioData-PT/Ready4BioDataManagement | website
• posit-conf-2023 posit-conf-2023/managing-os-project | website
• Fred Hutch Data Science Lab fhdsl/Ethical_Data_Handling_for_Cancer_Research | website
• Fred Hutch Data Science Lab fhdsl/NIH_Data_Sharing | website

FAIR data

• carpentries-incubator carpentries-incubator/fair-bio-practice | website
• carpentries-incubator carpentries-incubator/fair-for-leaders | website
• ELIXIR-Norway Training ELIXIR-Norway-Training/fair-dm-lifesci-june-2022
• FAIRplus FAIRplus/the-fair-cookbook | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-repository-submission-dm-practices | website
• ELIXIR Europe Training elixir-europe-training/ELIXIR-TrP-FAIR-training-handbook | website
• ELIXIR Europe Training elixir-europe-training/ELIXIR-TrP-FAIR-Converge | website
• Institut Français de Bioinformatique (IFB) IFB-ElixirFr/IFB-FAIR-bioinfo-training | website
• Institut Français de Bioinformatique (IFB) IFB-ElixirFr/IFB-FAIR-data-training
• Sergio Martínez Cuesta semacu/20180223_ORCID_Chemistry_Cambridge
• FAIR-by-Design-Methodology FAIR-by-Design-Methodology/FAIR-by-Design_Book | website

Reproducibility

• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/reproducibility-tools | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/workshop-reproducible-research
• carpentries-incubator carpentries-incubator/managing-computational-projects | website
• carpentries-incubator carpentries-incubator/jekyll-pages-novice | website
• carpentries-incubator carpentries-lab/good-enough-practices | website
• Data Carpentry datacarpentry/rr-organization1 | website
• SIB Swiss Institute of Bioinformatics sib-swiss/reproducible-analysis-training | website
• ELIXIR Europe Training elixir-europe-training/ELIXIR-TrP-ContainersPython-CodeRep | website
• ELIXIR Europe Training elixir-europe-training/ELIXIR-TrP-LiterateProgrammingR-CodeRep | website
• jhudsl jhudsl/Reproducibility_in_Cancer_Informatics | website
• jhudsl jhudsl/Documentation_and_Usability | website

Statistics and machine learning

Data science

• Stephanie Hicks stephaniehicks/superwomen | website
• Hacking for Science h4sci/h4sci-course
• DataTalksClub DataTalksClub/data-engineering-zoomcamp
• Jose A Dianes jadianes/data-science-your-way | website
• Jose A Dianes jadianes/spark-r-notebooks | website
• Data Carpentry datacarpentry/spreadsheet-ecology-lesson | website
• Data Science in Practice DataScienceInPractice/Site | website
• Shawn Rhoads shawnrhoads/gu-psyc-347 | website
• NBIS - National Bioinformatics Infrastructure Sweden NBISweden/module-openrefine-dm-practices | website
• Pablo Casas pablo14/data-science-live-book | website
• Roger D. Peng rdpeng/artofdatascience
• UC Berkeley Data 8 data-8/textbook | website
• Federico Carrone unbalancedparentheses/data_science_in_julia_for_hackers | website
• UC Berkeley Data 100 DS-100/textbook | website
• Edwin Thoen EdwinTh/ADSwR | website
• tidyverse tidyverse/datascience-box | website
• Modern Data Science with R mdsr-book/mdsr-book.github.io
• The Turing Way the-turing-way/the-turing-way | website

Statistics

• Aedin Culhane aedin/PCAworkshop | website
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/experimental-design | website
• CRUK CI Bioinformatics Core bioinformatics-core-shared-training/IntroductionToStats | website
• carpentries-incubator carpentries-incubator/statistical-thinking-public-health | website
• Richard McElreath rmcelreath/stat_rethinking_2022
• SIB Swiss Institute of Bioinformatics sib-swiss/advanced-statistics
• SIB Swiss Institute of Bioinformatics sib-swiss/intro-bayesian-statistics-training
• SIB Swiss Institute of Bioinformatics sib-swiss/introduction-to-statistics-with-python-training
• SIB Swiss Institute of Bioinformatics sib-swiss/Introduction-to-statistics-with-R
• SIB Swiss Institute of Bioinformatics sib-swiss/statistics-and-machine-learning-training
• Richard McElreath rmcelreath/stat_rethinking_2023
• David Dalpiaz daviddalpiaz/appliedstats | website
• cambiotraining cambiotraining/corestats | website
• David Dalpiaz daviddalpiaz/r4sl | website
• Mojtaba Barzegari mbarzegary/educational-bayesian
• SIB Swiss Institute of Bioinformatics sib-swiss/Data-analysis-in-practice
• The Gulbenkian Training Programme in Bioinformatics GTPB/PSLS22 | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/PGDH19 | website
• The Gulbenkian Training Programme in Bioinformatics GTPB/PSLS20 | website
• Matthew B. Jané MatthewBJane/guide-to-effect-sizes-and-confidence-intervals | website
• Richard McElreath rmcelreath/stat_rethinking_2024
• Monash Data Fluency MonashDataFluency/r-linear | website
• OpenIntro OpenIntroStat/ims | website
• Allen Downey AllenDowney/ThinkBayes
• Måns Thulin mthulin/mswr-book
• A. Solomon Kurz ASKurz/Statistical_Rethinking_with_brms_ggplot2_and_the_tidyverse_2_ed | website
• Allen Downey AllenDowney/ThinkStats2 | website
• Daniel Kaplan dtkaplan/Lessons-in-statistical-thinking
• Oslo Centre for Biostatistics and Epidemiology ocbe-uio/teaching_mf9130e | website
• Oslo Centre for Biostatistics and Epidemiology ocbe-uio/course_med3007 | website
• Sébastien Wieckowski sbwiecko/intuitive_biostatistics | website

Machine learning

• Canadian Bioinformatics Workshops bioinformatics-ca/MLE_2021
• carpentries-incubator carpentries-incubator/machine-learning-novice-python | website
• carpentries-incubator carpentries-incubator/machine-learning-novice-sklearn | website
• fast.ai fastai/course20 | website
• SIB Swiss Institute of Bioinformatics sib-swiss/intro-machine-learning-training
• Phillip Lippe phlippe/uvadlc_notebooks | website
• carpentries-incubator carpentries-incubator/ml4bio-workshop | website
• Instill AI instillai/TensorFlow-Course
• Yury Kashnitsky Yorko/mlcourse.ai | website
• fast.ai fastai/course-nlp | website
• girafe.ai girafe-ai/ml-course
• Paderborn University - LEA upb-lea/reinforcement_learning_course_materials
• Lex Fridman lexfridman/mit-deep-learning | website
• cambiotraining cambiotraining/intro-machine-learning | website
• carpentries-incubator carpentries-incubator/data-science-ai-senior-researchers | website
• carpentries-incubator carpentries-incubator/deep-learning-intro | website
• Sven Degroeve sdgroeve/Machine-Learning-Course-2days
• Philip Bowsher philbowsher/Workshop-R-Tensorflow-Scientific-Computing
• Nicola Rennie nrennie/r-pharma-2023-tidymodels | website
• udlbook udlbook/udlbook
• bioinformatics.ca bioinformaticsdotca/MLE_2023
• SIB Swiss Institute of Bioinformatics sib-swiss/pytorch-practical-training
• Applied Machine Learning for Tabular Data aml4td/website | website
• posit-conf-2023 posit-conf-2023/python-modeling
• Emil Hvitfeldt EmilHvitfeldt/smltar | website
• Navid Nobani Naviden/ML-intro-with-Python
• mlr-org mlr-org/mlr3book | website
• Inria INRIA/scikit-learn-mooc | website
• posit::conf(2024) posit-conf-2024/vetiver | website
• posit::conf(2024) posit-conf-2024/ml-python | website
• Neuromatch Academy NeuromatchAcademy/course-content | website

Artificial intelligence

• Maxime Labonne mlabonne/llm-course | website
• Fred Hutch Data Science Lab fhdsl/AI_for_Decision_Makers | website
• Fred Hutch Data Science Lab fhdsl/AI_for_Efficient_Programming | website

Others

General

• Amanda Miotto amandamiotto/HackyHourBookmarks
• biodatascience biodatascience/compbio | website
• Bradley Boehmke bradleyboehmke/data-science-learning-resources
• Ming Tang crazyhottommy/getting-started-with-genomics-tools-and-resources
• Teaching materials at the Harvard Chan Bioinformatics Core hbctraining/Training-modules | website
• Genome Informatics Facility ISUgenomics/bioinformatics-workbook | website
• Melbourne Bioinformatics melbournebioinformatics/MelBioInf_docs
• Mike Lee AstrobioMike/AstrobioMike.github.io | website
• liulab-dfci liulab-dfci/bioinfo-combio
• Leighton Pritchard widdowquinn/Teaching-IBioIC-Intro-to-Bioinformatics | website
• Ujjwal Karn ujjwalkarn/DataScienceR
• Salvatore Raieli SalvatoreRa/tutorial
• Alex's Lemonade Stand Foundation AlexsLemonade/training-modules
• Andrea Telatin telatin/microbiome-bioinformatics | website
• Ronan Harrington rnnh/bioinfo-notebook | website
• Women In Bioinformatics and Data Science Latin America WomenBioinfoDataScLA/Workshops
• Common Fund Data Ecosystem nih-cfde/training-and-engagement | website
• Thomas Denecker thomasdenecker/FAIR_Bioinfo
• Eric C. Anderson eriqande/eca-bioinf-handbook
• Computational Biology and Bioinformatics at UCLouvain UCLouvain-CBIO/WSBIM1322 | website
• UC Davis Bioinformatics Core Training Page ucdavis-bioinformatics-training/2020-Bioinformatics_Prerequisites_Workshop | website
• posit-conf-2023 posit-conf-2023/devops
• BioinformaNicks BioinformaNicks/Bioinformatics-training-collection
• Sex Chromosome Lab SexChrLab/BioinformaticsIntroduction
• Harvard Informatics harvardinformatics/learning-bioinformatics-at-home
• gladstone-institutes gladstone-institutes/Bioinformatics-Workshops | website
• jhudsl jhudsl/Informatics_Research_Leadership | website
• Pachter Lab pachterlab/BI-BE-CS-183-2023