scrna-meta-analysis skillA
scrna-meta-analysis is agent-read markdown (skill) from ammawla/encode-toolkit: 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 (Ha.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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@git:20260920.6050003mdr add ammawla/encode-toolkit/scrna-meta-analysis@sha256:00853f93de97ae69Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_bzkmz4xfx7nhwazz)
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Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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
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