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geo-connector SKILL.md skillA

geo-connector from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/geo-connector@git:20260921.4ba10c6

Pins git:20260921.4ba10c6 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: plugin/skills/geo-connector/SKILL.md
Versions recorded: 5
Latest version: git:20260921.4ba10c6, committed Sep 21, 2026
First version recorded: Mar 12, 2026
Size: 14,805 bytes
Repository stars: 21
License: AGPL-3.0

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE and GEO data, find supplementary files from GEO, or link GEO series to ENCODE experiments for provenance tracking. Also use when the user mentions GEO, GSE, GSM, GPL, GDS, series matrix, SOFT format, or needs to find…

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

# Search and Cross-Reference NCBI GEO with ENCODE

## When to Use

- User wants to find complementary datasets in NCBI GEO to supplement ENCODE data
- User asks about "GEO", "Gene Expression Omnibus", "supplementary data", or "find related datasets"
- User needs to cross-reference ENCODE experiments with GEO series for additional replicates or conditions
- User wants to link ENCODE accessions to GEO/SRA identifiers for data sharing or citation
- Example queries: "find GEO datasets for pancreatic islet RNA-seq", "link this ENCODE experiment to GEO", "search GEO for complementary ATAC-seq data"

Query the Gene Expression Omnibus programmatically to find complementary datasets, cross-reference ENCODE experiments, and download metadata.

## Scientific Rationale

**The question**: "What additional expression or epigenomic datasets exist in GEO that complement my ENCODE analysis?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/geo-connector@sha256:4fb412be74f26cda

The line at the top of this page pins the label git:20260921.4ba10c6, 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.

Badge

[![mdr](https://markdownregistry.com/badge/art_ea4hik2wxefeucuu.svg)](https://markdownregistry.com/a/art_ea4hik2wxefeucuu)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 48 days.

version	committed	commit	size	audit
git:20260921.4ba10c6 latest	2026-09-21	4ba10c6	14,805 B	A	view · diff
git:20260920.6050003	2026-09-20	6050003	14,749 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	14,286 B	A	view · diff
git:20260321.5cfbcfd	2026-03-21	5cfbcfd	14,241 B	A	view · diff
git:20260312.665e731	2026-03-12	665e731	14,229 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (14805 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

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_ea4hik2wxefeucuu
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/geo-connector
GET https://markdownregistry.com/api/v1/blob/4fb412be74f26cdaabe4802649720283382fabb5240899934494270501dc6b25

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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