gseapy-gene-enrichment SKILL.md skillA
gseapy-gene-enrichment from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/gseapy-gene-enrichment@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/rnaseq/gseapy-gene-enrichment/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 16,350 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or edgeR for pathway-level interpretation.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# GSEApy — Gene Set Enrichment Analysis in Python ## Overview GSEApy provides Python implementations of GSEA and over-representation analysis (ORA) for interpreting gene expression changes at the pathway level. The `enrich` module queries the Enrichr API to test a gene list against 200+ databases (GO, KEGG, MSigDB Hallmarks, Reactome, WikiPathways). The `prerank` and `gsea` modules run the GSEA algorithm on a pre-ranked gene list or expression matrix — computing normalized enrichment scores (NES) and FDR values for each gene set. GSEApy integrates directly with pandas DataFrames from DESeq2 or scanpy differential expression output, making it the standard Python tool for pathway analysis in RNA-seq workflows. ## When to Use - Interpreting DESeq2 or edgeR differential expression results at pathway/GO-term level - Running fast ORA (over-representation analysis) against Enrichr's 200+ databases including GO, KEGG, and MSigDB Hallmarks - Performing GSEA prerank analysis on a log2-fold-change-ranked gene list without an expression matrix - Identifying enriched pathways in scRNA-seq cluster marker genes - Generating publication-ready enrichment dot plots and GSEA running-score plots …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/gseapy-gene-enrichment@sha256:9aff4b04ee447239The line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_q6ehvfsqigrq6yh2)
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Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 16,350 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 16,399 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 13,985 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 14,094 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16350 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_q6ehvfsqigrq6yh2 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/gseapy-gene-enrichment GET https://markdownregistry.com/api/v1/blob/9aff4b04ee447239caa91810cdd3d6dc6f4220c68f327b1ce93d6877a17c1426
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