accessibility-aggregation SKILL.md skillA
accessibility-aggregation from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/accessibility-aggregation@git:20260921.7231da8Pins 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
skills/accessibility-aggregation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260921.7231da8, committed Sep 21, 2026
- First version recorded
- Mar 8, 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
mdr add ammawla/encode-toolkit/accessibility-aggregation@sha256:8efa4fe2bf4ddfd0The 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.
[](https://markdownregistry.com/a/art_2t25fiwimvz7dvhu)
4 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 21, 2026, about one every 98 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:20260308.ca46af5 | 2026-03-08 | ca46af5 | 13,959 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 (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
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_2t25fiwimvz7dvhu 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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