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
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Install
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
Use cases: productivity
Reviews
Write a reviewNo reviews yet. Installed it? Reviews come from verified installers only. How reviews work
Permissions
What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.
- Tools
- No tools found
- Secrets
- None asked for
- Install scripts
- None found
- 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.
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Signals
- Stars
- 2
- Forks
- 0
- Open issues
- 0
- Last commit (this folder)
- Aug 29, 2026 (2 months 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
- 0.557score
scientific-visualization
phenixace
Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
chembl-bioactivity
phenixace
Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
hmmer-profile-search
phenixace
Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
research-router
phenixace
Route broad life-science research questions to the smallest useful set of Molemo skills.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
protein-structure
phenixace
Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
guided-workflows
phenixace
Create reviewable, researcher-approved plans from Molemo scientific tools.
SkillBFreshness: B★ 2Claude Code +9
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Cite this page
geo-series-matrix-import skill. Agent Mart. https://agentmart.dev/skills/phenixace-geo-series-matrix-import (last updated 2026-10-24)