single-cell-encode skillA
single-cell-encode is agent-read markdown (skill) from ammawla/encode-toolkit: 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 ty.
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
# 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@git:20260921.4ba10c6mdr add ammawla/encode-toolkit/single-cell-encode@sha256:5bbbf463798d14c8Pin 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_p2ooihc5ngip6srx)
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Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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
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