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accessibility-aggregation 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.

accessibility-aggregation 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/accessibility-aggregation@git:20260921.7231da8

Pins git:20260921.7231da8 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: plugin/skills/accessibility-aggregation/SKILL.md
Versions recorded: 3
Latest version: git:20260921.7231da8, committed Sep 21, 2026
First version recorded: Mar 12, 2026
Size: 14,988 bytes
Repository stars: 21
License: AGPL-3.0

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak set. Handles cross-lab variation, ATAC vs DNase platform differences, and ENCODE blocklist filtering.

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

## When to Use

- User wants to combine ATAC-seq or DNase-seq peaks across multiple experiments for a tissue
- User asks "where is chromatin accessible in my tissue?" or "build an open chromatin map"
- User needs to merge accessibility data from different labs, donors, or platforms (ATAC vs DNase)
- User wants a comprehensive set of open chromatin regions for regulatory element discovery
- Example queries: "aggregate ATAC-seq peaks for pancreas", "combine DNase-seq across donors", "find all accessible regions in liver"

# Aggregate Chromatin Accessibility Peaks Across Studies

Build a comprehensive map of open chromatin for a tissue/cell type by merging ATAC-seq and/or DNase-seq narrowPeak files from multiple ENCODE experiments.

## Scientific Rationale

**The question**: "Where is chromatin accessible in my tissue?"

Like histone marks, chromatin accessibility is a **detection question**. An open chromatin region detected in one donor but not another is still a real accessible site — individual variation, sequencing depth, and technical factors explain absence. We want the **union of all detections**.

### ATAC-seq vs DNase-seq
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/accessibility-aggregation@sha256:8efa4fe2bf4ddfd0

The line at the top of this page pins the label git:20260921.7231da8, 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_zi3vedxvp3ezgjn3.svg)](https://markdownregistry.com/a/art_zi3vedxvp3ezgjn3)

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

Versions

The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 97 days.

version	committed	commit	size	audit
git:20260921.7231da8 latest	2026-09-21	7231da8	14,988 B	A	view · diff
git:20260920.6050003	2026-09-20	6050003	14,675 B	A	view · diff
git:20260312.665e731	2026-03-12	665e731	13,959 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 (14988 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_zi3vedxvp3ezgjn3
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/accessibility-aggregation
GET https://markdownregistry.com/api/v1/blob/8efa4fe2bf4ddfd06f69d1cec3c4e19f9247b808dc797ac47936370047f760df

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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