bio-single-cell-clustering - Single-cell RNA-seq Clustering Analysis
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat and Scanpy
Tags
Updated: 2026-03-20Capabilities
Typical Inputs
Typical Outputs
What this skill does
- run PCA
- compute variance ratio
- visualize PCA
- determine number of PCs
- compute neighbors
- perform Leiden clustering
- perform Louvain clustering
- compute UMAP
- visualize UMAP
- compute tSNE
- visualize tSNE
- perform PAGA
Inputs
- preprocessed single-cell RNA-seq data
- H5AD file (Scanpy)
- RDS file (Seurat)
Outputs
- cluster assignments
- PCA coordinates
- UMAP coordinates
- tSNE coordinates
- cluster visualization plots
Requirements
- Python or R environment
- Scanpy library
- Seurat library