Alterlab Scanpy
Skill AktivStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata. Part of the AlterLab Academic Skills suite.
To enable researchers to perform standard exploratory analysis on single-cell RNA-seq data by providing a robust, well-documented workflow powered by the Scanpy toolkit.
Funktionen
- Standard single-cell RNA-seq analysis workflow
- Quality control and filtering
- Normalization and feature selection
- Dimensionality reduction (PCA, UMAP, t-SNE)
- Clustering and marker gene identification
- Cell type annotation guidance
- Publication-quality plot generation
- Trajectory inference and differential expression support
Anwendungsfälle
- Performing exploratory data analysis on new scRNA-seq datasets
- Identifying cell populations and marker genes
- Generating figures for scientific publications or presentations
- Benchmarking or validating scRNA-seq analysis pipelines
Nicht-Ziele
- Deep learning models for scRNA-seq (use scvi-tools)
- Data format questions (use anndata documentation)
- Advanced omics integration beyond single-cell RNA-seq
- Real-time analysis of large-scale genomic data streams
Praktiken
- Reproducible research
- Single-cell analysis best practices
- Data visualization standards
Voraussetzungen
- Python 3 environment
- Scanpy and its dependencies (pandas, numpy, matplotlib, etc.)
- Input data in a compatible format (.h5ad, 10X, CSV)
Trust
- warning:Issues AttentionThere are 2 open issues and 0 closed issues in the last 90 days, indicating slow maintenance engagement.
Code Execution
- info:LoggingThe script provides console output for progress and QC metrics, but does not implement a dedicated local audit log file for actions.
Execution
- info:Pinned dependenciesThe template script lists imports, but specific pinned versions or lockfiles for dependencies are not explicitly provided within the repository.
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsFührt das Vercel skills CLI (skills.sh) via npx aus — benötigt Node.js lokal und mindestens einen installierten skills-kompatiblen Agent (Claude Code, Cursor, Codex, …). Setzt voraus, dass das Repo dem agentskills.io-Format folgt.
Qualitätspunktzahl
Vertrauenssignale
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