cellxgene-context skillA
cellxgene-context is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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
# 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@git:20260321.5cfbcfdmdr add ammawla/encode-toolkit/cellxgene-context@sha256:3953cc0c269c1adaPin 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_5giv7pdx3ucotgf4)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260321.5cfbcfd latest | 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 (19378 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_5giv7pdx3ucotgf4 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/cellxgene-context GET https://markdownregistry.com/api/v1/blob/3953cc0c269c1ada061e7c7f3eb949347e0e4f0cf8c997fa790a62e4e2c4815a
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