bio-data-visualization-manhattan-qq-locuszoom SKILL.md skillA
bio-data-visualization-manhattan-qq-locuszoom 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-manhattan-qq-locuszoom@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-manhattan-qq-locuszoom/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,654 bytes
- Repository stars
- 662
- License
- MIT
Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling, and LD-aware regional rendering. Use when visualizing association results across the genome, comparing two traits, computing genomic inflation lambda, or zooming into a locus with LD coloring.
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: qqman 0.1.9 (R), CMplot 4.5+ (R), matplotlib 3.8+, pandas 2.2+, scipy 1.12+, plinkQC 0.3+. For locuszoom-style: locuszoomr 0.3+ (R) or pyranges + matplotlib.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
# Manhattan, QQ, and Locuszoom Plots
**"Plot my GWAS results"** -> Render per-variant -log10(p) across the genome (Manhattan), compare expected vs observed p quantiles (QQ + λGC), overlay two traits with mirrored axes (Miami), and zoom into a locus with LD-colored points + recombination rate + gene track (locuszoom). The choices that matter: significance thresholds, axis truncation for ultra-significant peaks, lead-SNP labeling, and LD reference selection for regional plots.
- R: `qqman::manhattan` / `qqman::qq` (Turner 2018), `CMplot::CMplot`, `locuszoomr::locus_plot`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-data-visualization-manhattan-qq-locuszoom@sha256:4882be805e6f7cd0The 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_7cj5gzijtrphmyuy)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: Frontmatter declares a description
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- 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
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- 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_7cj5gzijtrphmyuy GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-data-visualization-manhattan-qq-locuszoom GET https://markdownregistry.com/api/v1/blob/4882be805e6f7cd04de4fdb3a6f9b1b4700ff51dfb4c24bb876b061670eef916
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.