bio-data-visualization-volcano-and-ma-plots SKILL.md skillA
bio-data-visualization-volcano-and-ma-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-volcano-and-ma-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-volcano-and-ma-plots/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 21,568 bytes
- Repository stars
- 662
- License
- MIT
Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.
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: DESeq2 1.42+, EnhancedVolcano 1.20+, ggplot2 3.5+, ggrepel 0.9.5+, matplotlib 3.8+, numpy 1.26+, adjustText 1.1+, apeglm 1.28+, ashr 2.2+.
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.
# Volcano and MA Plots
**"Plot differential-expression results"** -> Place per-feature shrunken effect estimate on the x-axis and a significance measure (-log10 padj or -log10 p) on the y-axis. The decision space spans which effect estimate (raw vs shrunken), which significance measure (raw p vs adjusted vs s-value), how to encode categories (color by direction, not by gradient), how to label (top-N is rarely informative), and how to handle the tail (extreme p compresses the plot).
- R: `EnhancedVolcano::EnhancedVolcano()`, `ggplot2 + ggrepel`, `DESeq2::plotMA()`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-data-visualization-volcano-and-ma-plots@sha256:9bbbb994161247daThe 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_f2j6d2wcesujikiv)
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 (21568 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_f2j6d2wcesujikiv GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-data-visualization-volcano-and-ma-plots GET https://markdownregistry.com/api/v1/blob/9bbbb994161247daccf8fc326e6edd4193118f839f41accfc5ecddb1b1ecb8ea
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.