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. We then filter low-quality cells and genes, detect potential doublets with…
