Single-cell & Spatial
Heterogeneity at the resolution of single cells and tissue coordinates.
Lessons
02-01 · Scanpy Core Analysis
Full scRNA-seq in Scanpy: raw matrix to cell-type labels.
02-02 · Seurat Core Analysis
The R equivalent of the Scanpy pipeline (Seurat v5).
02-03 · Trajectory & Pseudotime
Reconstruct differentiation trajectories, pseudotime and RNA velocity.
02-04 · Cell–Cell Communication
Infer ligand–receptor communication networks with CellChat v2.
02-05 · Regulatory Network (pySCENIC)
Discover TF regulons and per-cell activity de novo.
02-06 · Spatial Transcriptomics
Clustering and spatial analysis that keeps tissue location.
02-07 · Pooled CRISPR Screens
Analyse pooled CRISPR screens with scRNA-seq readout.
02-08 · scRNA Disease Drug Discovery
Single-cell plus genetics for multi-omics target prioritisation.