Recipes and reference

Use this part when you already know the analysis context and want a short route, a troubleshooting answer, or a package/function lookup.

• Task recipes: RNA-seq, no-DEG GSEA, single-cell markers, protein IDs, genomic regions, multi-omics, and non-model organisms.
• Leading-edge and non-model organism details
• Frequently asked questions and troubleshooting
• Package and capability map
• Glossary, function index, citations, and versions
• Reference appendix

The recipes show how to move from a common input to the next decision. The engine, knowledge, evidence, visualization, and interpretation parts explain why that route is appropriate.