scanpy
K-Dense-AI/scientific-agent-skills
A comprehensive, scalable Python toolkit designed for end-to-end single-cell RNA-seq data analysis. It supports crucial steps including quality control (QC), normalization, dimensionality reduction (PCA, UMAP, t-SNE), cell clustering, and differential gene expression analysis. The skill provides ready-to-run scripts for analyzing various formats (e.g., .h5ad, 10X, R-native) and generating publication-quality visualizations and cell type annotations.