accessibility-aggregation skillA
accessibility-aggregation is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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
## 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 …
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How to install
mdr add ammawla/encode-toolkit/accessibility-aggregation@git:20260312.665e731mdr add ammawla/encode-toolkit/accessibility-aggregation@sha256:ce003bc092cf32f5Pin 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_zi3vedxvp3ezgjn3)
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Audit of the latest version
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- pass: Size between 200 bytes and 200 KB (13959 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
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- pass: No base64 blob over 200 characters
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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_zi3vedxvp3ezgjn3 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/accessibility-aggregation GET https://markdownregistry.com/api/v1/blob/ce003bc092cf32f5bc7cbc8bc6ece2bcb44aa0f236bc238b7c753c891bdd8636
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