How to Build a Single-Cell RNA-seq Analysis Pipeline with Scanpy for PBMC Clustering, Annotation, and Trajectory Discovery

Scanpy tutorial processes PBMC-3k single-cell RNA-seq data end to end, from QC and doublet removal to normalization and gene selection.

It scores cell-cycle and interferon-response programs, regresses technical effects, and reduces the data with UMAP and t-SNE.

Leiden clustering and marker-based annotation identify immune cell populations, while PAGA and diffusion pseudotime infer lineage structure.

The workflow saves a final AnnData object ready for downstream biological analysis.