scanpy - Single-cell RNA-seq data analysis using Scanpy
Scanpy is a Python toolkit built on AnnData for analyzing single-cell RNA-seq data, providing workflows from quality control to trajectory analysis.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Load single-cell RNA-seq datasets
- Perform quality control filtering
- Normalize and scale expression data
- Select highly variable genes
- Compute PCA UMAP and t-SNE
- Perform Leiden cell clustering
- Identify cluster marker genes
- Annotate cell types
- Infer cell trajectories
- Generate single-cell visualization plots
Inputs
- Single-cell RNA-seq data files
- 10X Genomics matrix files
- AnnData h5ad files
- CSV expression data files
- Marker gene lists
Outputs
- Processed AnnData h5ad files
- Cell metadata CSV files
- Gene metadata CSV files
- Publication-quality PDF plot files
Requirements
- Python environment
- scanpy package
- pandas package
- numpy package