bio-data-visualization-lollipop-protein-maps SKILL.md skillA
bio-data-visualization-lollipop-protein-maps from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-data-visualization-lollipop-protein-maps@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-data-visualization-lollipop-protein-maps/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 12,547 bytes
- Repository stars
- 662
- License
- MIT
Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.
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
## Version Compatibility
Reference examples tested with: maftools 2.18+, trackViewer 1.38+, g3-lollipop (JavaScript via R `g3viz` 1.2+), Bio.PDB 1.83+ (for domain coordinates). ProteinPaint is a hosted service.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name`
- Python: `pip show <package>` then `help(module.function)`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
# Lollipop / Needle Protein Maps
**"Plot mutations on a gene's protein"** -> Render a horizontal protein backbone with colored domain rectangles (from UniProt/Pfam/InterPro), then stack vertical lines ("stems") at mutated amino-acid positions, capped with circles ("lollipops") whose size reflects mutation count and whose color encodes variant class. The biological story is hotspot identification — a tall stack of recurrences at a single residue (e.g., KRAS G12, PIK3CA E545/H1047) is the visual signature of a driver mutation.
- R: `maftools::lollipopPlot`, `trackViewer::lolliplot`, `g3viz::g3Lollipop`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-data-visualization-lollipop-protein-maps@sha256:14965dd8a662bf77The line at the top of this page pins the label git:20260821.2d1b678, 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_elriobnrfgmh3v6v)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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 (12547 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_elriobnrfgmh3v6v GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-data-visualization-lollipop-protein-maps GET https://markdownregistry.com/api/v1/blob/14965dd8a662bf777c5d69b0844a9fa788a1158b696586da77e629140d63c558
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.