geo-dataset-discovery
Discover public NCBI GEO Series from a biological question with exact GSE-only query provenance, bounded metadata, study-design caveats, and an approved…
Skill by phenixace
Chalk Labs
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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-dataset-discovery
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: design, 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-dataset-discovery
What's inside
- Skill name
geo-dataset-discovery- Description
- Discover public NCBI GEO Series from a biological question with exact GSE-only query provenance, bounded metadata, study-design caveats, and an approved persistence workflow.
- 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 Dataset Discovery Use this skill when a researcher wants to find public expression or methylation studies before selecting data for a local analysis. ## Boundary - Search the NCBI GEO DataSets database through E-utilities and require exact `GSE[ETYP]` Series filtering. - Preserve the free-text query, organism, assay scope, minimum GEO sample count, source relevance order, query translation, accessions, retrieval time, and public links. - Keep the agent-callable preview to eight records. Persist up to twenty records only through a researcher-approved workflow. - Treat sample count as submitter metadata, not the number of independent biological replicates. - Do not score dataset quality, infer analysis readiness from a file extension, or treat GEO relevance as scientific priority. - Flag SuperSeries/SubSeries, overlapping cohorts, incomplete metadata, normalization state, subject design, batch structure, and raw-data availability for researcher review. - Discovery does not download or analyze expression data.
From phenixace/Molemo_WorkBench, MIT.
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- 0.557score
scientific-visualization
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Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
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protein-structure
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Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.
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hmmer-profile-search
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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
guided-workflows
phenixace
Create reviewable, researcher-approved plans from Molemo scientific tools.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
research-router
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Route broad life-science research questions to the smallest useful set of Molemo skills.
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chembl-bioactivity
phenixace
Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.554score
single-cell-analysis
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Validate local single-cell raw-count matrices and propose researcher-approved Scanpy QC, embedding, clustering, and marker exploration.
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clinical-trial-landscape
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Search ClinicalTrials.gov for a bounded trial landscape or review the posted tabular results of one exact NCT record.
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dna-variant-calling
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Preflight and run a bounded, researcher-approved paired-end short-read DNA alignment and candidate variant-calling workflow with local BWA, samtools, and…
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functional-analysis
phenixace
Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI…
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geo-series-matrix-import
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Inspect and import one official NCBI GEO Series Matrix through a researcher-approved, bounded local workflow while preserving sample metadata, values and…
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protein-analysis
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Analyze protein FASTA sequences with local sequence-derived calculations.
SkillBFreshness: B★ 2Claude Code +9
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-dataset-discovery skill. Agent Mart. https://agentmart.dev/skills/phenixace-geo-dataset-discovery (last updated 2026-10-24)