single-cell-encode SKILL.md skillA
single-cell-encode 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/single-cell-encode@git:20260921.4ba10c6Pins git:20260921.4ba10c6 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/single-cell-encode/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260921.4ba10c6, committed Sep 21, 2026
- First version recorded
- Mar 12, 2026
- Size
- 30,307 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell…
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
# Single-Cell ENCODE Data ## When to Use - User wants to find or analyze single-cell data (scRNA-seq, scATAC-seq, snRNA-seq) from ENCODE - User asks about "single-cell", "scRNA-seq", "scATAC-seq", "cell type annotation", or "single-nucleus" - User needs to integrate ENCODE single-cell data with bulk epigenomic profiles - User wants to identify cell-type-specific regulatory elements from single-cell chromatin accessibility - Example queries: "find scRNA-seq data in ENCODE for brain", "what snATAC-seq is available?", "integrate single-cell with bulk ChIP-seq" Help the user find and work with ENCODE single-cell genomics data, understand quality limitations relative to bulk assays, and integrate single-cell with bulk ENCODE profiles for cell-type-resolved regulatory analysis. ## Literature Foundation | # | Reference | Key Contribution | |---|-----------|-----------------| | 1 | Mawla & Huising 2019, Endocrinology, DOI:10.1210/en.2018-01037 (~200 cit) | Cross-study scRNA-seq meta-analysis revealing that only ~1-2% of heterogeneity-driving genes replicate across studies; TIN-based quality assessment; detection-limit awareness framework. PMC6609986. | …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/single-cell-encode@sha256:5bbbf463798d14c8The line at the top of this page pins the label git:20260921.4ba10c6, 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_p2ooihc5ngip6srx)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 48 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 30,307 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 30,208 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 29,092 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 29,125 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 29,195 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 (30307 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_p2ooihc5ngip6srx GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/single-cell-encode GET https://markdownregistry.com/api/v1/blob/5bbbf463798d14c8fef259bfc957126ff9958be2f288915fcc59de2f5dc88e0f
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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