compare-biosamples skillA
compare-biosamples is agent-read markdown (skill) from ammawla/encode-toolkit: Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs normal comparison, developmental time course, constitutive vs variable regulation, or multi-tissue data availability mapping. Handles batch effect detection, biosample hierarchy, and comparison design..
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
# Compare ENCODE Data Across Biosamples ## When to Use - User wants to compare ENCODE experiments across different tissues, cell lines, or biosamples - User asks about "tissue comparison", "cell-type differences", "tissue-specific enhancers", or "cross-tissue" - User needs to identify constitutive vs tissue-specific regulatory elements - User wants to map data availability across multiple biosamples before integrative analysis - Example queries: "compare H3K27ac between liver and pancreas", "what marks are tissue-specific?", "find constitutive promoters across all tissues" Help the user systematically compare data availability and experiments across different biosamples to identify tissue-specific regulatory patterns, constitutive elements, and cross-tissue differences. ## Scientific Rationale …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/compare-biosamples@git:20260920.6050003mdr add ammawla/encode-toolkit/compare-biosamples@sha256:2bd267f47a53cf9dPin 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_jrdb2kpakshpdxo2)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 29,606 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 27,153 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 27,177 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 (29606 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_jrdb2kpakshpdxo2 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/compare-biosamples GET https://markdownregistry.com/api/v1/blob/2bd267f47a53cf9d41852658018d2aba5f7b6cdc9a66f8edebea91c4daa33e83
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