cellxgene-context SKILL.md skillA
cellxgene-context 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/cellxgene-context@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/cellxgene-context/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 20,077 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger on: CellxGene, single-cell atlas, cell type expression, Census, cell type specificity, single-cell context, scRNA-seq atlas.
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
# Integrating CellxGene Census Single-Cell Data with ENCODE Bulk Experiments Bridge bulk ENCODE functional genomics data with cell-type-specific expression from the CellxGene Census, the largest unified single-cell RNA-seq atlas, to resolve cell-type contributions to regulatory element activity. ## Scientific Rationale **The question**: "Which specific cell types within my tissue drive the regulatory signals I see in bulk ENCODE data?" ENCODE provides deeply sequenced bulk functional genomics (ChIP-seq, ATAC-seq, Hi-C) across hundreds of biosamples. But bulk data from a tissue like "pancreas" is a mixture of acinar cells (~80%), duct cells (~10%), endocrine cells (~5%), and others. An H3K27ac peak in bulk pancreas could be driven by any of these cell types. CellxGene Census provides cell-type-resolved expression data from 50M+ single-cell observations across thousands of datasets, enabling deconvolution of bulk ENCODE signals. ### The Bulk-to-Single-Cell Bridge | Bulk ENCODE Signal | Single-Cell Question | CellxGene Answer | |-------------------|---------------------|-----------------| …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/cellxgene-context@sha256:7086b6a93e843974The 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_5giv7pdx3ucotgf4)
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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 | 20,077 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 19,355 B | A | view · diff |
| git:20260321.5cfbcfd | 2026-03-21 | 5cfbcfd | 19,378 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 19,378 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 (20077 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_5giv7pdx3ucotgf4 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/cellxgene-context GET https://markdownregistry.com/api/v1/blob/7086b6a93e843974631b13ec7dd2dcaa2ff7fa3e425b24504dd0f7e764228a51
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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