geo-connector skillA
geo-connector is agent-read markdown (skill) from ammawla/encode-toolkit: 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 expr.
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
# 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
mdr add ammawla/encode-toolkit/geo-connector@git:20260321.5cfbcfdmdr add ammawla/encode-toolkit/geo-connector@sha256:1934693a4fb304abPin 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_ea4hik2wxefeucuu)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260321.5cfbcfd latest | 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
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14241 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_ea4hik2wxefeucuu GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/geo-connector GET https://markdownregistry.com/api/v1/blob/1934693a4fb304ab63e12b77f33b80035f1359e1f298eec68330b3fb657a0566
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