histone-aggregation skillA
histone-aggregation is agent-read markdown (skill) from ammawla/encode-toolkit: Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with confidence annotations. Handles cross-lab batch effects, broad vs narrow marks, 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
# Aggregate Histone ChIP-seq Peaks Across Studies ## When to Use - User wants to combine histone ChIP-seq peaks across multiple ENCODE experiments for a tissue or cell type - User asks "where is H3K27ac in pancreas?" or "build a histone mark map for liver" - User needs a union peak set from multiple donors, labs, or replicates - User wants to create a consensus binding map from multiple ChIP-seq datasets - Example queries: "aggregate all H3K4me3 peaks in brain", "combine histone marks across donors", "build enhancer map from H3K27ac data" Build a comprehensive map of histone mark binding for a tissue/cell type by merging narrowPeak files from multiple ENCODE experiments into a union peak set. ## Scientific Rationale **The question**: "Does my tissue have this histone mark, and at what genomic locations?" …
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How to install
mdr add ammawla/encode-toolkit/histone-aggregation@git:20260312.665e731mdr add ammawla/encode-toolkit/histone-aggregation@sha256:558250f85c5c2d3dPin 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_zlmc6zazsyfaf2we)
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Versions
Audit of the latest version
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- pass: Size between 200 bytes and 200 KB (16952 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zlmc6zazsyfaf2we GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/histone-aggregation GET https://markdownregistry.com/api/v1/blob/558250f85c5c2d3df757386bc59a2906d75ae17aa5cfb9811da09f878a25b14c
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