index.md

Tutorials

The tutorials are Jupyter notebooks. Each one opens the outputs of a bundled example, so you can read them here with their stored results, or run them yourself on the same example after a Docker check or a native run. They are executed in continuous integration against freshly produced example outputs, so the code on this site is code that runs.

Notebook	What you learn	Example it reads
Your first result	What a completed run contains, how peptides map to study groups, what a blank cell means	CAMPI
QC, replicates and PCA	Coverage, completeness, replicate CV and when PCA is eligible	Synthetic three-acquisition study
Community and function	Unipept taxonomy, eggNOG annotation and the peptide to protein evidence network	CAMPI community
Matched DNA and RNA	What specimen-matched candidates add, and the ledger that explains every inclusion	CAMPI with synthetic molecular values

Run a tutorial yourself

Produce the example outputs once (each example refuses to overwrite an existing folder):

python tools/run_tutorials.py --layout       # the example commands, in order
export FASTALAKE_TUTORIAL_DATA=$PWD/tutorial_data
python tools/run_tutorials.py --check        # executes every notebook against those outputs

Then open any notebook in docs/tutorials/ with Jupyter. The first cell reads FASTALAKE_TUTORIAL_DATA; point it at your own run directory to apply the same analysis to your study.