Frequently Asked Questions

What is this handbook for?

It provides predictable navigation, method-oriented protocols, teaching figures, and companion source files for common bioinformatics workflows.

Can I run the code directly?

Review each protocol page first. Most scripts expect input files, species settings, or package dependencies that are described in the relevant workflow.

Where are the companion files?

Use the notebook/sources/ directory. Each protocol page links to its companion folder and individual files.

How should I use it?

Start with the topic overview, read the protocol, then adapt the companion scripts to your own dataset and analysis environment.