multi-omics-integration skillA
multi-omics-integration is agent-read markdown (skill) from ammawla/encode-toolkit: 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 type-specific.
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
# 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@git:20260920.6050003mdr add ammawla/encode-toolkit/multi-omics-integration@sha256:02aef3d632f7e176Pin 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_c3vepthv7urkpnug)
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Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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
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