Create & manage databases
Best practices for project structure, naming, and multiple DBs per project.
Data & Retrieval
Managing your Entrez API key
Create and set an Entrez API key to speed up article retrieval.
How PubTator3 provides gene mentions
Where annotations come from, how synonyms/IDs are normalized, and caveats to expect.
Gene Set Libraries
Use your own GMT
Validate and load custom gene sets; version and share with collaborators.
Exploring Enrichr libraries
What's inside the Enrichr collections and when to use each library.
Ranking & Statistics
Understand statistics
Hypergeometric test, odds ratios, z-scores, and FDR control (BH, BY, etc.).
Ranking genes: GF-IDF vs Count
When to prefer GF-IDF or raw counts; tradeoffs and interpretations.
Results & Comparison
Interpret section-level signals
Use the section plot to separate background mentions from results-driven evidence.
Share & compare
Export TSV/HTML plots, compare runs across libraries, and track parameters.
Deep Dives
Understanding the Info Panel
Use the info panel to inspect current processes, your project folder, or log messages.