Home / ammawla / encode-toolkit · GitHub

search-encode SKILL.md skillA

This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.

search-encode from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/search-encode@git:20260921.4ba10c6

Pins 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: skills/search-encode/SKILL.md
Versions recorded: 4
Latest version: git:20260921.4ba10c6, committed Sep 21, 2026
First version recorded: Mar 8, 2026
Size: 24,093 bytes
Repository stars: 21
License: AGPL-3.0

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.

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

# 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

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/search-encode@sha256:3b42894205944951

The 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.

Badge

[![mdr](https://markdownregistry.com/badge/art_wku77jclcpkjmrw2.svg)](https://markdownregistry.com/a/art_wku77jclcpkjmrw2)

2 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 4 versions of this file, between Mar 8, 2026 and Sep 21, 2026, about one every 65 days.

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:20260308.ca46af5	2026-03-08	ca46af5	23,793 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

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

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_wku77jclcpkjmrw2
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/search-encode
GET https://markdownregistry.com/api/v1/blob/3b4289420594495199209cc262d6970cdda5a1c7a4b277c2609af2a8f74fbebe

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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