scrna-meta-analysis SKILL.md skillA
scrna-meta-analysis from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/scrna-meta-analysis@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
plugin/skills/scrna-meta-analysis/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 31,084 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq data across donors, labs, and platforms. Follows the Mawla et al. 2019 framework for assessing cross-study reproducibility, TIN-based quality filtering, and detection-limit-aware interpretation. Handles batch correction…
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
# Cross-Study Meta-Analysis of scRNA-seq Data ## When to Use - User wants to perform meta-analysis across multiple single-cell RNA-seq datasets - User asks about "scRNA-seq meta-analysis", "dataset integration", "batch correction", or "cross-study comparison" - User needs to harmonize cell type annotations across studies from different labs - User wants to build reference atlases or identify conserved cell populations across datasets - Example queries: "integrate 5 scRNA-seq datasets from different labs", "harmonize cell type labels across studies", "meta-analyze single-cell data for pancreas" Integrate multiple ENCODE scRNA-seq datasets for a tissue/cell type into a unified cell atlas with reproducibility-aware quality assessment. ## Scientific Rationale **The question**: "What cell types and transcriptional programs are present in my tissue, and which findings are reproducible across studies?" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/scrna-meta-analysis@sha256:00853f93de97ae69The line at the top of this page pins the label git:20260920.6050003, 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_bzkmz4xfx7nhwazz)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 64 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 31,084 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 30,250 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 30,262 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 30,311 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 (31084 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
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_bzkmz4xfx7nhwazz GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/scrna-meta-analysis GET https://markdownregistry.com/api/v1/blob/00853f93de97ae69b69ecb7f71522b804740e81628a203ff504224f39ff0daa3
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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