bio-differential-expression-de-visualization SKILL.md skillA
bio-differential-expression-de-visualization 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-differential-expression-de-visualization@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-differential-expression-de-visualization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,541 bytes
- Repository stars
- 662
- License
- MIT
Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and…
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+, edgeR 4.0+, limma 3.58+, ggplot2 3.5+, pheatmap 1.0+, RColorBrewer 1.1+, ggrepel 0.9+, EnhancedVolcano 1.20+, matrixStats 1.2+
Before using code patterns, verify installed versions match. If versions differ:
- 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.
# DE Visualization
**"Make the standard DE figure panel"** -> Use built-in functions or thin wrappers to produce diagnostic plots (dispersion, p-value histogram, PCA, sample distance) and result plots (MA, volcano, heatmap of top DE genes, per-gene counts), interpreted as diagnostics of the underlying model.
## Scope
This skill covers DE-specific built-in plots and immediate wrappers. For richer customization:
- Custom volcano/MA with apeglm-shrunken LFC and ggrepel labelling -> `data-visualization/volcano-and-ma-plots`
- PCA / UMAP / t-SNE customization -> `data-visualization/dimensionality-reduction-plots`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-differential-expression-de-visualization@sha256:d542bb86a7a8e26cThe 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_fc7csyfin2ip5nqj)
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 (20541 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_fc7csyfin2ip5nqj GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-differential-expression-de-visualization GET https://markdownregistry.com/api/v1/blob/d542bb86a7a8e26cfc8bd8e016077cc20bf9592f41d9f12ab8c87ba4426f54e4
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.