Scanpy tutorials

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scanpy-tutorials is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. Please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

• Using other kNN libraries in Scanpy
• Plotting with Marsilea
• Preprocessing and clustering
• Preprocessing and clustering 3k PBMCs (legacy workflow)
• Integrating data using ingest and BBKNN
• Core plotting functions
• Customizing Scanpy plots
• Using dask with Scanpy
• How to preprocess UMI count data with analytic Pearson residuals
• Analysis and visualization of spatial transcriptomics data
• Integrating spatial data with scRNA-seq using scanorama
• Trajectory inference for hematopoiesis in mouse