scanpy

Scanpy: Single-Cell Analysis Overview Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. When to Use This Skill This skill should be used when: Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats) Performing quality control on scRNA-seq datasets Creating UMAP, t-SNE, or PCA visualizations Identifying cell clusters and finding marker genes Annotating cell types based on gene expression Conducting trajectory inference or pseudotime analysis Generating publication-quality single-cell plots Quick Start Show more