bio-differential-expression-batch-correction SKILL.md skillA
bio-differential-expression-batch-correction 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-batch-correction@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-batch-correction/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 22,889 bytes
- Repository stars
- 662
- License
- MIT
Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk)…
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: sva 3.50+ (includes ComBat + ComBat_seq), DESeq2 1.42+, edgeR 4.0+, limma 3.58+, RUVSeq 1.36+, ggplot2 3.5+, harmony 1.2+ (single-cell context only)
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.
# Batch Effect Correction
**"Remove the batch effect before DE"** -> Almost always WRONG. Include batch as a covariate in the design formula (`~ batch + condition`) so DESeq2/edgeR/limma model it without subtracting. Subtraction is for visualization only.
## The Single Most Important Modern Insight -- The Nygaard 2016 cardinal sin
Nygaard, Rødland, Hovig 2016 *Biostatistics* 17(1):29-39, "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses." Translation: **never run ComBat (or ComBat-seq, or `removeBatchEffect`, or SVA-subtract-then-test) and then run DE on the corrected matrix.**
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-differential-expression-batch-correction@sha256:faf6262cb7ca779aThe 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_73ck2cgvky6r4woz)
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 (22889 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_73ck2cgvky6r4woz GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-differential-expression-batch-correction GET https://markdownregistry.com/api/v1/blob/faf6262cb7ca779a3d10f62e479911f27269283ae8b1311d06bca8ab6b12f05a
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.
More from pku-yuangroup/openai4s
Every file in pku-yuangroup/openai4s