Skill · em Dados, IA e pesquisa

geo-database

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Procedência

Antes de instalar

2 arquivos · 44,5 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/geo-database/.

d=".claude/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/geo-database/.

d="$HOME/.claude/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/geo-database/.

d=".agents/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/geo-database/.

d="$HOME/.agents/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/geo-database/.

d=".agents/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/geo-database/.

d="$HOME/.gemini/antigravity-cli/skills/geo-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/geo-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/geo_reference.md" "$u/references/geo_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.geo-database

Prévia do SKILL.md

---
name: geo-database
description: "Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis."
---

# GEO Database

## Overview

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.

## When to Use This Skill

This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.

## Core Capabilities

### 1. Understanding GEO Data Organization

GEO organizes data hierarchically using different accession types:

**Series (GSE):** A complete experiment with a set of related samples
- Example: GSE123456
- Contains experimental design, samples, and overall study information
- Largest organizational unit in GEO
- Current count: 264,928+ series

**Sample (GSM):** A single experimental sample or biological replicate
- Example: GSM987654
- Contains individual sample data, protocols, and metadata
- Linked to platforms and series
- Current count: 8,068,632+ samples

**Platform (GPL):** The microarray or sequencing platform used
- Example: GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array)
- Describes the technology and probe/feature annotations
- Shared across multiple experiments
- Current count: 27,739+ platforms

**DataSet (GDS):** Curated collections with consistent formatting
…

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