bio-protein-clustering-pangenome SKILL.md skillA
bio-protein-clustering-pangenome from fmschulz/omics-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fmschulz/omics-skills/bio-protein-clustering-pangenome@git:20261001.bf5afd6Pins git:20261001.bf5afd6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fmschulz/omics-skills
- Path
skills/bio-protein-clustering-pangenome/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- May 13, 2026
- Size
- 9,401 bytes
- Repository stars
- 11
- License
- MIT
Cluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, copy number, or core and accessory content across genomes.
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
# Bio Protein Clustering Pangenome
Cluster proteins into orthogroups and derive pangenome matrices.
## Instructions
Tool guides and versions: [docs/README.md](docs/README.md).
1. After clustering, build and validate the complete small-to-large comparison bundle with:
```bash
uv run --script skills/bio-protein-clustering-pangenome/scripts/build_pangenome_artifacts.py \
orthogroups.tsv --genomes genomes.tsv --marker-catalog marker_catalog.tsv \
--marker-hits marker_hits.tsv --ncrna ncRNA_census.tsv \
--out results/bio-protein-clustering-pangenome
```
`orthogroups.tsv` is a long table with one row per protein: `orthogroup, protein_id, genome, contig, order, start, end`. Build it from the clustering output (OrthoFinder `Orthogroups.tsv` is wide and must be melted) joined with gene coordinates from the gene-calling GFF; `order` is the gene's rank along its contig. `genomes.tsv` has `genome, role (query|reference), genome_size, contig_count, n50, gene_count, coding_density, gc`. The marker catalog has `category, family_id, family_name`; marker hits have `genome, family_id, protein_id, e_value`; the ncRNA census uses the `/bio-gene-calling` columns. The…
…Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-protein-clustering-pangenome@sha256:1cd9cefcec44fd55The line at the top of this page pins the label git:20261001.bf5afd6, 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_num75bvfhr2tyepf)
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Versions
The registry has recorded 6 versions of this file, between May 13, 2026 and Oct 1, 2026, about one every 28 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 9,401 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 8,269 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 7,840 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 8,350 B | A | view · diff |
| git:20260711.5ae6f6f | 2026-07-11 | 5ae6f6f | 7,458 B | A | view · diff |
| git:20260513.82d3d6a | 2026-05-13 | 82d3d6a | 6,351 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 (9401 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
fmschulz/omics-skills · 11 stars · license MIT · pushed 2026-10-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_num75bvfhr2tyepf GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-protein-clustering-pangenome GET https://markdownregistry.com/api/v1/blob/1cd9cefcec44fd552c3d1dce1e6e0643fd60c87c52598a3bc0d6cf2e62046628
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.