hic-aggregation skillA
hic-aggregation is agent-read markdown (skill) from ammawla/encode-toolkit: Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolution-aware anchor matching, cross-lab variation, and Hi-C-specific quality metrics..
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 Hi-C Chromatin Contacts Across Studies ## When to Use - User wants to build a comprehensive catalog of chromatin loops from multiple Hi-C experiments - User asks "what regions are in 3D contact in my tissue?" or "aggregate loop calls across donors" - User needs a union catalog of BEDPE loops with resolution-aware anchor matching - User wants to identify high-confidence loops supported by multiple experiments - Example queries: "aggregate Hi-C loops for K562", "combine chromatin contacts across labs", "find consensus TAD boundaries in liver" Build a comprehensive catalog of chromatin loops for a tissue/cell type by merging BEDPE loop calls from multiple ENCODE Hi-C experiments. ## Scientific Rationale **The question**: "What regions are in 3D physical contact in my tissue?" Like histone marks and accessibility, chromatin loops are a **detection question**. If a loop between Region A and Region B is detected in one donor but not another, the contact is still real — individual variation, sequencing depth, and computational resolution explain absence. We want the **union of all detected contacts**. ### Key Concepts …
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How to install
mdr add ammawla/encode-toolkit/hic-aggregation@git:20260921.7231da8mdr add ammawla/encode-toolkit/hic-aggregation@sha256:eb8dc582c49a321dPin 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_cgou3k3n54zpdoxq)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.7231da8 latest | 2026-09-21 | 7231da8 | 23,379 B | A | view · diff |
| git:20260921.4ba10c6 | 2026-09-21 | 4ba10c6 | 23,070 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 23,124 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 22,051 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 22,058 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 (23379 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_cgou3k3n54zpdoxq GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/hic-aggregation GET https://markdownregistry.com/api/v1/blob/eb8dc582c49a321d06c9a05be30021db1412a84c82bbbbcf91c741a7881d64ce
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