multi-omics-integration SKILL.md skillA
multi-omics-integration 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/multi-omics-integration@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
skills/multi-omics-integration/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 33,924 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and which transcription factors control them?" by layering expression, chromatin accessibility, histone marks, and TF binding data. Follows the Mawla et al. 2023 framework for cross-assay integration of islet cell…
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
# Multi-Omics Integration of ENCODE Data ## When to Use - User wants to integrate multiple ENCODE data types (RNA-seq + ATAC-seq + ChIP-seq) for a tissue - User asks about "multi-omics", "integrative analysis", "regulatory landscape", or "layer epigenomic data" - User needs to build a comprehensive view of active enhancers, promoters, and TF binding in a tissue - User wants to combine expression with chromatin state to identify cell-type-specific regulatory networks - Example queries: "integrate all ENCODE data for pancreas", "build a regulatory landscape for liver", "combine RNA-seq and ChIP-seq to find active enhancers" Layer RNA-seq, ATAC-seq, Histone ChIP-seq, and TF ChIP-seq data from ENCODE to build a comprehensive regulatory landscape for a tissue or cell type. ## Scientific Rationale **The question**: "What regulatory elements are active in my tissue, and how do expression, chromatin accessibility, histone marks, and TF binding converge to define cell identity?" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/multi-omics-integration@sha256:02aef3d632f7e176The line at the top of this page pins the label git:20260920.6050003, 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_c3vepthv7urkpnug)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 49 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 33,924 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 32,860 B | A | view · diff |
| git:20260920.f517fca | 2026-09-20 | f517fca | 32,911 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 32,910 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 32,892 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 (33924 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_c3vepthv7urkpnug GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/multi-omics-integration GET https://markdownregistry.com/api/v1/blob/02aef3d632f7e1769390326161f1e0fd0606f0efaf6b984d5c891198f750597e
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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