scanpy - Single-cell RNA-seq data analysis with Scanpy
Scanpy provides Python tools for single-cell RNA-seq data analysis, including quality control, clustering, visualization, and trajectory inference.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Load single-cell datasets
- Perform quality control filtering
- Normalize gene expression data
- Reduce data dimensionality
- Cluster single cells
- Identify marker genes
- Annotate cell types
- Infer cell trajectories
- Generate single-cell plots
Inputs
- scRNA-seq data files (.h5ad, 10X, CSV)
- Quality control parameters
- Marker gene lists
- Batch annotations
Outputs
- Processed AnnData files (.h5ad)
- Cell and gene metadata CSV files
- Single-cell visualization plots (PDF)
Requirements
- Python environment
- Scanpy package
- Pandas package
- NumPy package