Skill · em Dados, IA e pesquisa

scvi-tools

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential…

Procedência

Antes de instalar

9 arquivos · 95,1 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/scvi-tools/.

d=".claude/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/scvi-tools/.

d="$HOME/.claude/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/scvi-tools/.

d=".agents/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/scvi-tools/.

d="$HOME/.agents/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/scvi-tools/.

d=".agents/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.gemini/antigravity-cli/skills/scvi-tools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/scvi-tools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/differential-expression.md" "$u/references/differential-expression.md" \
  -o "$d/references/models-atac-seq.md" "$u/references/models-atac-seq.md" \
  -o "$d/references/models-multimodal.md" "$u/references/models-multimodal.md" \
  -o "$d/references/models-scrna-seq.md" "$u/references/models-scrna-seq.md" \
  -o "$d/references/models-spatial.md" "$u/references/models-spatial.md" \
  -o "$d/references/models-specialized.md" "$u/references/models-specialized.md" \
  -o "$d/references/theoretical-foundations.md" "$u/references/theoretical-foundations.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$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.scvi-tools

Prévia do SKILL.md

---
name: scvi-tools
description: This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression,…
---

# scvi-tools

## Overview

scvi-tools is a comprehensive Python framework for probabilistic models in single-cell genomics. Built on PyTorch and PyTorch Lightning, it provides deep generative models using variational inference for analyzing diverse single-cell data modalities.

## When to Use This Skill

Use this skill when:
- Analyzing single-cell RNA-seq data (dimensionality reduction, batch correction, integration)
- Working with single-cell ATAC-seq or chromatin accessibility data
- Integrating multimodal data (CITE-seq, multiome, paired/unpaired datasets)
- Analyzing spatial transcriptomics data (deconvolution, spatial mapping)
- Performing differential expression analysis on single-cell data
- Conducting cell type annotation or transfer learning tasks
- Working with specialized single-cell modalities (methylation, cytometry, RNA velocity)
- Building custom probabilistic models for single-cell analysis

## Core Capabilities

scvi-tools provides models organized by data modality:

### 1. Single-Cell RNA-seq Analysis
Core models for expression analysis, batch correction, and integration. See `references/models-scrna-seq.md` for:
- **scVI**: Unsupervised dimensionality reduction and batch correction
- **scANVI**: Semi-supervised cell type annotation and integration
- **AUTOZI**: Zero-inflation detection and modeling
- **VeloVI**: RNA velocity analysis
- **contrastiveVI**: Perturbation effect isolation

### 2. Chromatin Accessibility (ATAC-seq)
Models for analyzing single-cell chromatin data. See `references/models-atac-seq.md` for:
- **PeakVI**: Peak-based ATAC-seq analysis and integration
- **PoissonVI**: Quantitative fragment count modeling
- **scBasset**: Deep learning approach with motif analysis
…

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