Tutorials

See also

For more tutorials featureing scanpy and other scverse ecosystem tools, check out the curated set of tutorials at scverse.org/learn

Basic workflows

• Basics
  • Preprocessing and clustering
  • Preprocessing and clustering 3k PBMCs (legacy workflow)
  • Integrating data using ingest and BBKNN

Visualization

• Plotting
  • Core plotting functions
  • Customizing Scanpy plots

Trajectory inference

See also

For more powerful tools for analysing single cell dynamics, check out the Scverse ecosystem packages:

• CellRank

• Dynamo

• Trajectories
  • Trajectory inference for hematopoiesis in mouse

Spatial data

See also

For more up-to-date tutorials on working with spatial data, see:

• SquidPy tutorials

• SpatialData tutorials

• Scverse ecosystem spatial tutorials

• Spatial
  • Analysis and visualization of spatial transcriptomics data
  • Integrating spatial data with scRNA-seq using scanorama

Experimental

• Experimental
  • How to preprocess UMI count data with analytic Pearson residuals
  • Using dask with Scanpy

Older tutorials

A number of older tutorials can be found at:

• The scanpy_usage repository