geo-database SKILL.md skillA
geo-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/geo-database@git:20260528.3e3f998Pins git:20260528.3e3f998 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/databases/geo-database/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.3e3f998, committed May 28, 2026
- Size
- 17,136 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
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
# GEO Gene Expression Omnibus Database ## Overview GEO (Gene Expression Omnibus) is NCBI's public repository for high-throughput functional genomics data, containing 200,000+ datasets (series) from microarrays, RNA-seq, ChIP-seq, methylation, and proteomics experiments. GEOparse provides a Python interface for downloading and parsing GEO records (GSE series, GPL platforms, GSM samples) while NCBI E-utilities enables programmatic search across GEO's metadata. ## When to Use - Searching for publicly available gene expression datasets by organism, tissue, disease, or experimental condition - Downloading and parsing a specific GEO series (GSE) with its expression matrix and sample metadata - Extracting sample annotation tables (e.g., treatment groups, clinical covariates) for meta-analysis - Loading microarray expression data (GPL platform-annotated probes) into a tidy DataFrame - Retrieving all GEO experiments associated with a gene or pathway of interest - Building automated pipelines that download and process GEO datasets for downstream analysis - For single-cell RNA-seq data at scale, use `cellxgene-census`; for aligned reads, download FASTQ from ENA/SRA instead …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/geo-database@sha256:134049c375180157The line at the top of this page pins the label git:20260528.3e3f998, 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_462szquiwrvs6cvf)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
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 (17136 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_462szquiwrvs6cvf GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/geo-database GET https://markdownregistry.com/api/v1/blob/134049c375180157960a91c57a635e0becdadea1f7085cdabbcb34114f896e22
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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