deseq2-differential-expression SKILL.md skillA
deseq2-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/deseq2-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/deseq2-differential-expression/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 25,818 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.
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
# DESeq2 Differential Expression Analysis (R/Bioconductor) ## Overview DESeq2 is the Bioconductor R package for differential gene expression analysis from bulk RNA-seq count data. It fits a negative binomial generalized linear model per gene, estimates dispersion parameters using empirical Bayes shrinkage across genes, and tests differential expression using Wald tests (two-group) or likelihood ratio tests (complex designs). DESeq2 is the R gold standard for RNA-seq DE analysis, with native Bioconductor integration for seamless import from Salmon (tximeta/tximport), featureCounts, or HTSeq. ## When to Use - Identifying differentially expressed genes between two experimental conditions (treated vs. control, disease vs. healthy) from bulk RNA-seq count data - Analyzing multi-factor designs that account for batch effects or covariates (e.g., `~ batch + condition`) - Testing complex hypotheses with interaction terms (e.g., time × treatment) or reduced models using likelihood ratio tests (LRT) - Importing Salmon pseudoalignment output via tximeta or tximport for transcript-level uncertainty propagation …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/deseq2-differential-expression@sha256:edfd8f74fcbb44ecThe 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_ejrkurgw43wzfts7)
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Versions
The registry has recorded 5 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 25,818 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 25,867 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 23,443 B | A | view · diff |
| git:20260610.7af4766 | 2026-06-10 | 7af4766 | 23,685 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 23,388 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 (25818 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_ejrkurgw43wzfts7 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/deseq2-differential-expression GET https://markdownregistry.com/api/v1/blob/edfd8f74fcbb44ec074fea0be057a3cd6364ac3556baf6f53f79153b301aa914
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