methylation-aggregation skillA
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methylation-aggregation is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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 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@git:20260921.7231da8mdr add ammawla/encode-toolkit/methylation-aggregation@sha256:ac62a8738c77fc35Pin 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_t73dolfxpwgost3u)
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Versions
| 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:20260920.992a807 | 2026-09-20 | 992a807 | 22,795 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_t73dolfxpwgost3u GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/methylation-aggregation GET https://markdownregistry.com/api/v1/blob/ac62a8738c77fc35ae481c3c068aeee28b25f7993b091a1545ba5ae12b3b10c4
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