search-encode skillA
search-encode is agent-read markdown (skill) from ammawla/encode-toolkit: Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays, organs, cell lines, or targets..
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
# Search ENCODE Data ## When to Use - User wants to find ENCODE experiments matching specific criteria (assay, organ, cell type, target) - User asks "what ENCODE data exists for [tissue/target/assay]?" - User wants to explore available data before downloading - User needs to find specific file types (BED, BAM, bigWig) across experiments - User wants to know how many experiments exist for a condition - User asks about available assays, organisms, or biosamples in ENCODE Help the user find ENCODE experiments and files. Use the appropriate tools based on what they need. ## Search Strategy 1. **Finding experiments**: Use `encode_search_experiments` with filters: - `assay_title`: "Histone ChIP-seq", "ATAC-seq", "total RNA-seq", "polyA plus RNA-seq", "TF ChIP-seq", "Hi-C", "CUT&RUN", "WGBS", etc. - `organ`: "pancreas", "brain", "liver", "heart", "kidney", "lung", etc. - `biosample_type`: "tissue", "cell line", "primary cell", "organoid" - `biosample_term_name`: specific name like "GM12878", "HepG2", "K562" - `target`: ChIP/CUT&RUN target like "H3K27me3", "H3K4me3", "CTCF", "p300" - `organism`: "Homo sapiens" (default) or "Mus musculus" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/search-encode@git:20260921.4ba10c6mdr add ammawla/encode-toolkit/search-encode@sha256:3b42894205944951Pin 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_ongsbgcsmfusxuir)
1 badge views in 30 days
Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 24,093 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 24,065 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 23,766 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 23,793 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 (24093 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_ongsbgcsmfusxuir GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/search-encode GET https://markdownregistry.com/api/v1/blob/3b4289420594495199209cc262d6970cdda5a1c7a4b277c2609af2a8f74fbebe
Your agent 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.