All skills & plugins / Scientific Agent Skills (K-Dense)

pathway-enrichment

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis

Type: Skill by K-Dense Inc.
Catalog: Scientific Agent Skills (K-Dense)
Source: K-Dense-AI/scientific-agent-skills/skills/pathway-enrichment (6 files scanned)
Install and details: Agent Skills Index entry
License: MIT (SKILL.md frontmatter)
Signals: Bundled scripts

Pre-approved tools

No allowed-tools or tools list in its SKILL.md, command or agent files, so the agent asks before using tools as usual.

Hooks

No hooks.

MCP servers and apps

None.

Bundled code

1 code file (Python):

pathway-enrichment/scripts/run_enrichment.py

Network calls

No HTTP or socket call pattern found in the code.

Starts other programs

No subprocess, exec or eval pattern found.

Credentials referenced

No key, token or secret environment variable found in code or MCP config.

Static scan of commit 5f2bc03 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.