methylation-aggregation SKILL.md skillA
methylation-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/methylation-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/methylation-aggregation/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260921.7231da8, committed Sep 21, 2026
- First version recorded
- Mar 12, 2026
- Size
- 23,722 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data into tissue-level methylation profiles. Handles coverage filtering, identifies hypomethylated regions (HMRs) and partially methylated domains (PMDs), and manages cross-lab variation.
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 DNA Methylation Data Across Studies ## When to Use - User wants to build a tissue-level DNA methylation landscape from multiple WGBS experiments - User asks "where is DNA methylated in brain?" or "find hypomethylated regions across donors" - User needs to identify HMRs (hypomethylated regions), UMRs, or PMDs from aggregated WGBS data - User wants per-CpG weighted methylation averages from multiple experiments - Example queries: "aggregate WGBS data for liver", "build methylation map across donors", "find unmethylated CpG islands in pancreas" Build a comprehensive methylation landscape for a tissue/cell type by merging WGBS bedMethyl files from multiple ENCODE experiments. ## Scientific Rationale **The question**: "What is the DNA methylation state across the genome in my tissue?" DNA methylation is **fundamentally different** from histone marks and accessibility: | Property | Histone/Accessibility | DNA Methylation | |----------|----------------------|-----------------| | Signal type | Binary (bound/open or not) | Continuous (0-100% methylated) | | Default state | Unmarked | ~70-80% methylated (CpG context) | …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/methylation-aggregation@sha256:ac62a8738c77fc35The 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_6ylr3koyci55zhmf)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 64 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.7231da8 latest | 2026-09-21 | 7231da8 | 23,722 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 23,321 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 22,795 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 22,800 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 (23722 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_6ylr3koyci55zhmf GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/methylation-aggregation GET https://markdownregistry.com/api/v1/blob/ac62a8738c77fc35ae481c3c068aeee28b25f7993b091a1545ba5ae12b3b10c4
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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