integrative-analysis 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.
integrative-analysis 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/integrative-analysis@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/integrative-analysis/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 30,230 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample…
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
# Integrative Analysis of ENCODE Data ## When to Use - User wants to combine multiple ENCODE experiments for cross-dataset analysis - User asks about "integrating", "combining", or "comparing" experiments - User wants to overlay histone marks with accessibility or expression data - User needs to plan a multi-omic analysis using ENCODE data - User asks about peak overlap, differential binding, or signal correlation - User wants to perform ChromHMM segmentation using ENCODE histone data Help the user combine multiple ENCODE experiments for cross-dataset or multi-omic analysis. This skill covers the full integration workflow: from defining the question and selecting compatible experiments, through choosing the right integration strategy and tools, to validating results and documenting provenance. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| | ENCODE Phase 3 (2020) | Nature | Registry of 926,535 candidate cis-regulatory elements; integrative analysis framework across 5,992 experiments | [10.1038/s41586-020-2493-4](https://doi.org/10.1038/s41586-020-2493-4) | ~1,656 | …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/integrative-analysis@sha256:7e6144f1026701c5The 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_n4jbqfsxllczopwe)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 65 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 30,230 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 29,090 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 28,961 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 28,955 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 (30230 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_n4jbqfsxllczopwe GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/integrative-analysis GET https://markdownregistry.com/api/v1/blob/7e6144f1026701c5b3e26d2eab7b4515adb6df6130ba521cc53b5f1f8d4fc02d
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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