Datasets from our lessons
The exact real datasets our projects use. Open these to follow along, or to practice the same workflow on your own.
The airway dataset
Human airway smooth-muscle cells treated with dexamethasone (Himes et al., 2014). The classic teaching dataset for differential expression.
Open GSE52778 on GEO →Human gene sequences
Real human genes used in the Python and Bash projects. The lessons fetch them by RefSeq accession (NM_000207, NM_000518, NM_000484); explore each gene here:
Insulin (INS) →Beta-globin (HBB) →
APP (Alzheimer's) →
Palmer Penguins
Real measurements of 344 penguins across three species - the friendly dataset behind the R project. Installs as an R package.
Palmer Penguins docs →Practice gene tables
Three small CSV files the R lessons read straight from the web: a gene table, a gene-by-sample count table and a sample sheet. Values are made up for practice, but shaped like a real RNA-seq experiment.
practice-genes.csv →practice-counts.csv →
practice-samples.csv →
PyDESeq2 example data
The compact count matrix the flagship RNA-seq lesson runs on, so everything works instantly in your browser.
PyDESeq2 documentation →Where the data lives
The public databases professional bioinformaticians use every day. Free, open, and enormous.
NCBI
The U.S. hub for sequences, genes, and genomes - including GenBank and the Entrez search system.
ncbi.nlm.nih.gov →Ensembl
Richly annotated genomes for humans and many other species, with a friendly genome browser.
ensembl.org →GEO
Gene Expression Omnibus - a vast archive of expression experiments (including RNA-seq) you can reanalyze.
GEO →Free tools to work in
Everything you need to start, without spending a cent or - for the first three - installing anything.
Google Colab
Run Python notebooks in your browser, free. What our lessons use so you can start with zero setup.
Open Colab →Galaxy
Run real bioinformatics tools (alignment, QC, and more) through a point-and-click web interface - no command line needed.
usegalaxy.org →VS Code
A free desktop editor for your scripts and projects. We have a step-by-step setup guide.
Set up VS Code →Bioconductor
The home of R's biology packages - DESeq2, edgeR, limma, and hundreds more.
bioconductor.org →R for Data Science (2e)
The free online book most R learners graduate to after our R series: data wrangling, plotting and good workflow habits with the tidyverse.
r4ds.hadley.nz →Biopython
The Python toolkit for working with sequences and biological file formats.
biopython.org →Rosalind
Learn bioinformatics by solving bite-sized coding problems - a fun way to practice.
rosalind.info →NCBI BLAST
Search the world's sequence databases for matches to your DNA or protein, free in the browser. The tool behind our Sequence Alignment mini-course.
Open BLAST →EMBL-EBI Tools
Free web tools for pairwise and multiple sequence alignment (Clustal Omega, MUSCLE) and more - no install needed.
ebi.ac.uk tools →When you get stuck
Everyone does. Start with our beginner Help & FAQ; the rest is where the wider community goes for answers.
Beginner Help & FAQ
New and stuck? Start here: is it free, do I need to install anything, what is Colab, can I use VS Code, and what to do when a cell shows an error.
Open Help & FAQ →Cheat sheets
Free one-page quick references: command line & samtools, file formats, conda & Git, and stats & DESeq2.
Open cheat sheets →Reading R error messages
The six errors R beginners meet most, what each one means and how to fix it, with broken code you can run and repair in your browser.
First steps in RStudio →Posit Community
A friendly forum for R, RStudio and tidyverse questions, run by the makers of RStudio.
forum.posit.co →Our Facebook page
Updates, tips, and a place to connect with the BioNexus Hub community.
Follow BioNexus Hub →Ready to put these to use?
The roadmap walks you through exactly how to use these datasets and tools, step by step - from your first line of code to a finished analysis.
Start the roadmap →