Skill · em Dados, IA e pesquisa

scanpy

Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/scanpy
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
1 download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

6 arquivos · 48,8 KB · inclui 2 scripts que executam: assets/analysis_template.py, scripts/qc_analysis.py

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/scanpy/.

d=".claude/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/scanpy/.

d="$HOME/.claude/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/scanpy/.

d=".agents/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/scanpy/.

d="$HOME/.agents/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/scanpy/.

d=".agents/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.gemini/antigravity-cli/skills/scanpy"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scanpy"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/analysis_template.py" "$u/assets/analysis_template.py" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/plotting_guide.md" "$u/references/plotting_guide.md" \
  -o "$d/references/standard_workflow.md" "$u/references/standard_workflow.md" \
  -o "$d/scripts/qc_analysis.py" "$u/scripts/qc_analysis.py" \
  -o "$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.scanpy

Prévia do SKILL.md

---
name: scanpy
description: "Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis."
---

# Scanpy: Single-Cell Analysis

## Overview

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.

## When to Use This Skill

This skill should be used when:
- Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
- Performing quality control on scRNA-seq datasets
- Creating UMAP, t-SNE, or PCA visualizations
- Identifying cell clusters and finding marker genes
- Annotating cell types based on gene expression
- Conducting trajectory inference or pseudotime analysis
- Generating publication-quality single-cell plots

## Quick Start

### Basic Import and Setup

```python
import scanpy as sc
import pandas as pd
import numpy as np

# Configure settings
sc.settings.verbosity = 3
sc.settings.set_figure_params(dpi=80, facecolor='white')
sc.settings.figdir = './figures/'
```

### Loading Data

```python
…

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