hic-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.
hic-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/hic-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
plugin/skills/hic-aggregation/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260921.7231da8, committed Sep 21, 2026
- First version recorded
- Mar 12, 2026
- Size
- 23,379 bytes
- Repository stars
- 21
- License
- AGPL-3.0
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.
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
# 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 …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/hic-aggregation@sha256:eb8dc582c49a321dThe 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_zviwjou2ved3oall)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 48 days.
| 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.ce7840d | 2026-09-20 | ce7840d | 22,051 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zviwjou2ved3oall GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/hic-aggregation GET https://markdownregistry.com/api/v1/blob/eb8dc582c49a321d06c9a05be30021db1412a84c82bbbbcf91c741a7881d64ce
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.
More from ammawla/encode-toolkit
Every file in ammawla/encode-toolkit