AI Blocks › Research a topic properly
Gene list pathway finder
Give it a gene list or ranked genes. Get the biological pathways that stand out, explained in plain terms.
Gene list pathway finder is a free AI skill for the job "Research a topic properly". Give the instructions to an AI assistant that supports the required files and tools, then review its output.
Free · No account · MIT licence · Made by K-Dense · Level: advanced
Made by K-Dense. See the original on GitHub; we copied it as it is, with its licence.
What it does
A list of genes becomes a short answer about which biology stands out. Give it a list of significant genes or a full ranked table, and it finds the pathways and gene sets that show up more than chance allows. The first choice is the method. A thresholded hit list goes through over-representation testing. A full ranked table goes through GSEA, which keeps the ranking. It also covers per-sample scores. It then guides database choice, background gene sets, ID fixes and removing near-duplicate results. Results come as tables and figures you can use in a paper. It needs Python with several scientific packages, and online lookups need a network.
You give it
- A gene list or ranked gene table
- Species
- Gene set database preference (optional)
- A background gene list (optional)
You get
- Enriched pathways and gene sets
- A method choice with reasons
- Cleaned, deduplicated results
- Tables and plots for a report
Use it when
- You have a list of differentially expressed genes and ask what they have in common.
- You have a ranked result table and want GSEA done properly.
- Your pathway results look repetitive and need cleaning up.
- You are unsure whether to use a hit list or a ranked list.
How to use it
- Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
- Ask for the job in your own words. Your AI opens the skill when it fits.
- It works best when your AI can run code.