pydeseq2 SKILL.md skillA
pydeseq2 from foryourhealth111-pixel/vibe-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add foryourhealth111-pixel/vibe-skills/pydeseq2@git:20260226.1632f40Pins git:20260226.1632f40 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- foryourhealth111-pixel/vibe-skills
- Path
bundled/skills/pydeseq2/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260226.1632f40, committed Feb 26, 2026
- Size
- 16,105 bytes
- Repository stars
- 3,805
- License
- Apache-2.0
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
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
## Overview
PyDESeq2 is a Python implementation of DESeq2 for differential expression analysis with bulk RNA-seq data. Design and execute complete workflows from data loading through result interpretation, including single-factor and multi-factor designs, Wald tests with multiple testing correction, optional apeGLM shrinkage, and integration with pandas and AnnData.
## When to Use This Skill
This skill should be used when:
- Analyzing bulk RNA-seq count data for differential expression
- Comparing gene expression between experimental conditions (e.g., treated vs control)
- Performing multi-factor designs accounting for batch effects or covariates
- Converting R-based DESeq2 workflows to Python
- Integrating differential expression analysis into Python-based pipelines
- Users mention "DESeq2", "differential expression", "RNA-seq analysis", or "PyDESeq2"
## Quick Start Workflow
For users who want to perform a standard differential expression analysis:
```python
import pandas as pd
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats
# 1. Load data
counts_df = pd.read_csv("counts.csv", index_col=0).T # Transpose to samples × genes
…Read the whole file at its exact version.
How to install
mdr add foryourhealth111-pixel/vibe-skills/pydeseq2@sha256:055b202f5a8cb867The line at the top of this page pins the label git:20260226.1632f40, 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_ul7y2cda3ev2r3tx)
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Versions
The registry has recorded 1 version of this file, committed on Feb 26, 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 (16105 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
foryourhealth111-pixel/vibe-skills · 3,805 stars · license Apache-2.0 · pushed 2026-11-07 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ul7y2cda3ev2r3tx GET https://markdownregistry.com/api/v1/resolve?ref=foryourhealth111-pixel/vibe-skills/pydeseq2 GET https://markdownregistry.com/api/v1/blob/055b202f5a8cb8671f26652d37b16440ef02332790902a89e7ffc42da0642c15
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.
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