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

In this tutorial, we perform an advanced single-cell RNA-seq analysis workflow using Scanpy on the PBMC-3k benchmark dataset.

We start by loading the dataset, inspecting its structure, and applying quality control checks to evaluate gene counts, total counts, mitochondrial content, and ribosomal gene signals.