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compare-biosamples 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.

compare-biosamples 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/compare-biosamples@git:20260920.6050003

Pins 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: skills/compare-biosamples/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 8, 2026
Size: 29,606 bytes
Repository stars: 21
License: AGPL-3.0

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs normal comparison, developmental time course, constitutive vs variable regulation, or multi-tissue data availability mapping. Handles batch effect detection, biosample hierarchy, and comparison design.

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

# Compare ENCODE Data Across Biosamples

## When to Use

- User wants to compare ENCODE experiments across different tissues, cell lines, or biosamples
- User asks about "tissue comparison", "cell-type differences", "tissue-specific enhancers", or "cross-tissue"
- User needs to identify constitutive vs tissue-specific regulatory elements
- User wants to map data availability across multiple biosamples before integrative analysis
- Example queries: "compare H3K27ac between liver and pancreas", "what marks are tissue-specific?", "find constitutive promoters across all tissues"

Help the user systematically compare data availability and experiments across different biosamples to identify tissue-specific regulatory patterns, constitutive elements, and cross-tissue differences.

## Scientific Rationale
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/compare-biosamples@sha256:2bd267f47a53cf9d

The 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.

Badge

[![mdr](https://markdownregistry.com/badge/art_jrdb2kpakshpdxo2.svg)](https://markdownregistry.com/a/art_jrdb2kpakshpdxo2)

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

Versions

The registry has recorded 3 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 98 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	29,606 B	A	view · diff
git:20260920.992a807	2026-09-20	992a807	27,153 B	A	view · diff
git:20260308.ca46af5	2026-03-08	ca46af5	27,177 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 (29606 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_jrdb2kpakshpdxo2
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/compare-biosamples
GET https://markdownregistry.com/api/v1/blob/2bd267f47a53cf9d41852658018d2aba5f7b6cdc9a66f8edebea91c4daa33e83

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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