bio-data-visualization-upset-plots SKILL.md skillA
bio-data-visualization-upset-plots 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-upset-plots@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-upset-plots/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 12,001 bytes
- Repository stars
- 662
- License
- MIT
Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.
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: ComplexUpset 1.3+ (R, Krassowski), UpSetR 1.4.0 (last 2019 release; effectively unmaintained), upsetplot 0.9+ (Python).
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.
# UpSet Plots
**"Show set intersections for 4+ sets"** -> Replace Venn diagrams (which become illegible past 4 sets) with UpSet (Lex 2014 *IEEE TVCG* 20:1983). The display: a matrix of dots indicating which sets participate in each intersection, with a vertical bar above each column showing intersection size and horizontal bars on the left showing per-set total size. Sort by intersection size (cardinality) for "biggest overlaps first" or by degree (number of sets) for grouped layout.
- R: `ComplexUpset::upset` (Krassowski; ggplot2-native, **recommended**), `UpSetR::upset` (Conway 2017; legacy, unmaintained)
- Python: `upsetplot.UpSet`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-data-visualization-upset-plots@sha256:5d6209caedbb1ec4The 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_ncuf5rhja72tw3ul)
3 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
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- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12001 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_ncuf5rhja72tw3ul GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-data-visualization-upset-plots GET https://markdownregistry.com/api/v1/blob/5d6209caedbb1ec43f468fba22ae0c287dba1d8e9a7042e0fdc66c91fe19958a
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.