integrative-analysis skillA
integrative-analysis is agent-read markdown (skill) from ammawla/encode-toolkit: 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, cross-or.
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
# 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 | …
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How to install
mdr add ammawla/encode-toolkit/integrative-analysis@git:20260321.5cfbcfdmdr add ammawla/encode-toolkit/integrative-analysis@sha256:2f5c4bfdc2355e43Pin 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_34bb2t4gaifmy3eb)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260321.5cfbcfd latest | 2026-03-21 | 5cfbcfd | 28,961 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 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 (28961 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_34bb2t4gaifmy3eb GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/integrative-analysis GET https://markdownregistry.com/api/v1/blob/2f5c4bfdc2355e43d428e3306f09956d05715ec04b318a76c34d2ebfc4e356c8
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