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geo-series-matrix-import

Inspect and import one official NCBI GEO Series Matrix through a researcher-approved, bounded local workflow while preserving sample metadata, values and…

Skill by phenixace

IndexedMIT★ 2
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Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/phenixace-geo-series-matrix-import

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

Inspect and import one official NCBI GEO Series Matrix through a researcher-approved, bounded local workflow while preserving sample metadata, values and provenance without treating processed measurements as raw counts.

Use cases: productivity

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Permissions

What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

Tools
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Secrets
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Install scripts
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Runs as
Python package

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/geo-series-matrix-import

What's inside

Skill name
geo-series-matrix-import
Description
Inspect and import one official NCBI GEO Series Matrix through a researcher-approved, bounded local workflow while preserving sample metadata, values and provenance without treating processed measurements as raw counts.
License
MIT
Instructions
15 lines in SKILL.md · view on GitHub

Before installing

  • Ships executable scripts

Files (4)

  • SKILL.md
  • openai.yaml · agents/
  • handler.py · scripts/
  • skill.json

SKILL.md (first lines)

# GEO Series Matrix Import

Use this skill after a researcher selects an exact GSE accession and wants to bring its submitter-processed matrix into the local workspace.

## Boundary

- Resolve only the official HTTPS mirror of the accession's GEO `matrix/` directory.
- If multiple platform-specific matrices exist, require one exact filename before approval.
- Keep the Agent-callable step to directory and source-size preflight. Download only after local researcher approval.
- Enforce compressed, uncompressed, sample, feature and matrix-cell limits while parsing gzip content line by line.
- Preserve the original compressed file, source URL, retrieval time, SHA-256, expression table, sample metadata and manifest.
- Treat Series Matrix values as submitter-processed measurements with unknown transformation until the record and publication are reviewed.
- Do not send the imported matrix directly to a raw-count PyDESeq2 workflow, infer experimental groups, map probes, remove batches or fit a statistical model.

From phenixace/Molemo_WorkBench, MIT.

More from phenixace/Molemo_WorkBench

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Forks
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Last commit (this folder)
Aug 29, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

License
MIT
Repository
github.com/phenixace/Molemo_WorkBench
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

More from phenixace

Cite this page

geo-series-matrix-import skill. Agent Mart. https://agentmart.dev/skills/phenixace-geo-series-matrix-import (last updated 2026-10-24)