pydeseq2-differential-expression SKILL.md skillA
pydeseq2-differential-expression from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pydeseq2-differential-expression@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/rnaseq/pydeseq2-differential-expression/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 15,357 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
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
# PyDESeq2 Differential Expression Analysis ## Overview PyDESeq2 is a Python reimplementation of the R DESeq2 package for differential gene expression analysis from bulk RNA-seq count data. It fits negative binomial generalized linear models per gene, estimates dispersion with empirical Bayes shrinkage, and performs Wald tests with Benjamini-Hochberg FDR correction. This skill covers the full pipeline from raw counts to publication-ready result tables and visualizations. ## When to Use - Identifying differentially expressed genes between two or more experimental conditions from bulk RNA-seq - Performing two-group comparisons (e.g., treated vs control) with proper statistical testing - Running multi-factor designs that account for batch effects or covariates (e.g., `~batch + condition`) - Applying log2 fold change shrinkage (apeGLM) for ranking and visualization - Use `omics-plotting` SKILL after DE for publication-quality plots of differential expression results - Converting R-based DESeq2 workflows to a pure Python environment - Integrating DE analysis into larger Python bioinformatics pipelines (e.g., with scanpy, pandas) …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pydeseq2-differential-expression@sha256:845c36707043d64bThe line at the top of this page pins the label git:20260929.7a7d60f, 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_4q2z2c2pn7hxeqtb)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 15,357 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 15,406 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 13,249 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 13,909 B | A | view |
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 (15357 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4q2z2c2pn7hxeqtb GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pydeseq2-differential-expression GET https://markdownregistry.com/api/v1/blob/845c36707043d64b2e3432cf04971ab63b2533656911dbcebd651a58194025b2
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.