Do-It-Yourself
Training
Free self-paced bioinformatics training - Software Carpentry, Data Carpentry, and online tutorials for R, Python, Unix, and genomics analysis.
Comprehensive Training Platforms
Large multi-topic resources - the best starting points for self-directed bioinformatics learning.
Comprehensive lessons for beginners covering Unix Shell, Git, Python, R, and R for Reproducible Scientific Analysis. Domain-specific lessons via Data Carpentry: Genomics · Ecology · Geospatial Analysis
Extensive online workbook with videos and worked examples covering command line basics, HPC, GitHub, BLAST, experimental design, RNA-seq, single-cell, genome assembly, variant discovery (FreeBayes and GATK), metagenomics, ATAC-seq, and data visualisation.
Wealth of workflows, resources, a help forum, and Slack team. Carpentries workshops available: Data science with Bioconductor · Bulk RNA-seq · Single-cell RNA-seq · Intro to Bioconductor
Wide variety of free online courses including bioinformatics, Bash, Python, R and RStudio - organised by universities, GitHub, and institutes including the Wellcome Institute. Most courses can be audited free; certificates available for a fee.
Resources by Topic
Individual courses and collections for specific analysis types - colour-coded by category.
Library Carpentry R Course
Designed for beginners to learn R basics, including data manipulation, visualisation, and statistical analysis.
Advanced R Documentation
Hadley Wickham's comprehensive guide to advanced R programming concepts and practices.
Statistical Inference for Biology
A Carpentries Incubator project covering statistical modeling for biological data analysis.
RNA-Seq Analysis
Multiple entry points for bulk RNA-seq - from QC and alignment through to differential gene expression and publication figures.
Single-Cell RNA-Seq Training
Introductory course for single-cell RNA-seq analysis.
Spatial Transcriptomics
Course by S.M. McClatchy covering spatial transcriptomics analysis.
Experimental Design Training
Two complementary courses - basic experimental design principles and a statistically rigorous approach to study design.
QTL Mapping
Resources for quantitative trait locus mapping in model organisms and humans.
glittr - Training Repo Finder
Search engine for Git repositories containing bioinformatics training material. Filter and sort by topic, popularity, and recency - a fast way to find quality course content on GitHub.
Corey Schafer - Python YouTube
143+ Python tutorial videos from absolute basics through to intermediate topics including object-oriented programming, data visualisation with Matplotlib, and data science workflows.
SIB Training Collection
Curated collection of bioinformatics training materials from the Swiss Institute of Bioinformatics - all in GitHub repositories, free to use, and written in Markdown or similar. Searchable by topic.
learnR4free
Curated directory of completely free R learning resources - books, courses, podcasts, and tutorials organised by difficulty level and topic.
Swirl - Learn R in R
Interactive R courses that run directly in your R console - no browser needed. Covers R programming basics, data analysis, regression, and more. Great for absolute beginners.
Happy Git with R
Jenny Bryan's beloved guide to using Git and GitHub from R and RStudio - covers installation, workflows, branching, and common pain points, written specifically for data analysts.
Git for Scientists
Practical Git tutorial written for researchers - covers the core workflow (clone, add, commit, push, pull), branching, and collaborating on GitHub with a science audience in mind.
Reproducible Workflows for Data Science
UBC course covering reproducible and trustworthy workflows - dependency management, containerisation, licensing, testing, and CI/CD pipelines for research software.
Analysing CRISPR Screens with edgeR
Free bookdown tutorial covering the full workflow for analysing CRISPR screen data using edgeR - from count processing through to differential abundance testing and visualisation in R.
shRNA-seq Analysis - WEHI
Worked tutorial from the Walter and Eliza Hall Institute covering shRNA-seq analysis using edgeR and limma - read counting, normalisation, differential representation testing, and interpretation.
Pipelines & Workflows
Scale beyond single scripts - workflow languages used in production bioinformatics.
Snakemake
hover to exploreSnakemake
- Wildcards and expand() for scaling across samples
- Native conda & container integration per rule
- Cluster and cloud execution with minimal config changes
- DAG visualisation before running
- Extensive tutorial and worked genomics examples
Nextflow & nf-core
hover to exploreNextflow & nf-core
- Dataflow model - laptop, HPC, or cloud identically
- Native Docker, Singularity & conda support
- nf-core: RNA-seq, variant calling, scRNA-seq & more
- All pipelines include test datasets & full docs
- Active community Slack for support
WDL
hover to exploreWDL
- Portable, human-readable workflow specification
- Runs on Cromwell and miniWDL execution engines
- Widely used in genomics - Terra/Broad ecosystem
- Tutorials for building pipelines in genomics & beyond
Containers
hover to exploreContainers
- Pull and run existing tool containers instantly
- Build custom images for your own tools
- Singularity for HPC - no root access required
- Foundation of reproducible pipeline environments
Organisations Offering Free Training
Australian and international organisations running bioinformatics workshops - check their calendars for upcoming events.
QCIF Training
Live online workshops via Zoom covering bioinformatics, R, statistics, HPC, and machine learning. Free for staff and students at member universities; wider access available via Instats.
Statistical Comparisons Using R: Developed by QCIF/CaRST. Covers hypothesis testing, correlation analysis, ANOVA, and visualizing data. Prior R knowledge required.
Adelaide Bioinformatics Hub
Open-access lesson materials and workshop archives from the University of Adelaide Bioinformatics Hub.
ABACBS Workshops
Workshop archives from the Australian Bioinformatics and Computational Biology Society conferences.
Melbourne Bioinformatics (MBITE)
Extensive library of free self-paced online tutorials covering RNA-seq, variant calling, Galaxy, genome assembly, and more. National workshops run with Australian BioCommons are free to all Australian researchers.
Australian BioCommons
Hosts and co-delivers nationally free online workshops on Galaxy, Nextflow, Snakemake, and applied genomics. Full archive of past webinar recordings and training materials available on Zenodo. Also runs the National Bioinformatics Training Cooperative - a community for trainers across Australian research institutions.
Intersect Australia
Research technology training for member universities across NSW, ACT, and beyond. Covers HPC, data management, R, and Python. Primarily in-person or institutional-access - check with your institution.
Harvard Chan Bioinformatics Core (HBC)
All training materials freely available under CC BY 4.0. Covers R, shell scripting, bulk RNA-seq, single-cell RNA-seq, ChIP-seq, and more. Designed for wet-bench biologists moving into computation.
BIG Bioinformatics
Free online workshops in R and Python for biomedical science. Sessions are recorded and remain available after the course ends. Subscribe to their mailing list for upcoming dates.
Babraham Bioinformatics
Extensive library of training courses spanning basic data processing, RNA-Seq, ChIP-Seq, and network analysis.
EMBL-EBI Training
Extensive library of on-demand bioinformatics tutorials, courses, and recorded webinars. Free to access, with a sign-up option to track progress and build learning playlists.
Training Registries - TeSS & DReSA
Two complementary training registries for finding bioinformatics courses and events. TeSS (ELIXIR) aggregates courses from all ELIXIR nodes across Europe. DReSA is the Australasian equivalent - a search engine aggregating workshops across Australian and NZ research institutions.
Coursera Bioinformatics Specializations
Substantial, structured training tracks provided by institutions like UC San Diego and the Technical University of Denmark (DTU). Deep dives into algorithms and computational biology.
Rosalind
A platform for learning bioinformatics and programming through problem-solving. Provides substantial hands-on training scaling from basic Python to complex genomics algorithms.
Galaxy Training Network (GTN)
Massive collection of hands-on tutorials for analyzing data using the Galaxy platform. Covers transcriptomics, genomics, machine learning, and more with integrated compute resources.
Summer Institute in Statistical Genetics (SISG)
The renowned Bruce Weir SISG (at Georgia Tech) offers comprehensive modules in population, quantitative, and integrative genomics. Provides deep foundational training.
ISS / ISGW – Institute for Behavioral Genetics
The International Statistical Genetics Workshop (CU Boulder) has run for over 20 years through the Institute for Behavioral Genetics. Covers twin/family designs, GWAS, linkage analysis, and downstream genomic data analysis. Extensive archive of lectures and practicals freely available online.
SAGC – SA Genomics Centre
The South Australian Genomics Centre organises hands-on workshops on genomics topics in South Australia - a key local training provider for Adelaide-based researchers across all career stages.
Sydney Informatics Hub (SIH)
Research support, training, and expertise in data management, statistics, data science, software engineering, bioinformatics, and research computing for University of Sydney researchers and affiliates. Runs regular workshops open to the community.
COMBINE
The student-run Australian organisation for students in computational biology, bioinformatics, and related fields. Organises an annual symposium (as part of ABACBS), networking events, and a Slack community connecting students nationally.
ARDC - Australian Research Data Commons
Enables Australian researchers and industry access to nationally significant, data-intensive digital research infrastructure. Runs regular tech talks and training events focused on data management, research software, and digital infrastructure. Variety of free resources on working with data.
Monash Data Fluency
Community of researchers using data, based at Monash University. Provides training and community events covering data analysis, R, Python, and data management - with materials and recordings often publicly available.
ISCB Academy
The International Society for Computational Biology hosts regular webinars and workshops for members via the ISCB Academy. Covers cutting-edge computational biology, machine learning in genomics, and career development. Membership required for full access.
UWA Centre for Applied Bioinformatics
Virtual centre connecting researchers and bioinformaticians at UWA, Harry Perkins Institute, Telethon Kids Institute, and the Marshall Centre. Provides bioinformatics support and training across all career levels, from lab data analysis through to large-scale HPC studies.
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Bioinformatics, statistical genomics & computational biology - practical tools, learning resources, and expert guidance based in South Australia. We are a community that believes in accessible knowledge and learning together.