Tutorials

Clustering

For getting started, we recommend Scanpy’s reimplementation → tutorial: pbmc3k of Seurat’s [Satija15] clustering tutorial for 3k PBMCs from 10x Genomics, containing preprocessing, clustering and the identification of cell types via known marker genes.

http://falexwolf.de/img/scanpy_usage/170505_seurat/filter_genes_dispersion.png http://falexwolf.de/img/scanpy_usage/170505_seurat/louvain.png http://falexwolf.de/img/scanpy_usage/170505_seurat/NKG7.png http://falexwolf.de/img/scanpy_usage/170505_seurat/violin.png http://falexwolf.de/img/scanpy_usage/170505_seurat/cell_types.png

For more possibilities on visualizing marker genes: → tutorial: visualizing-marker-genes

https://scanpy-tutorials.readthedocs.io/en/latest//_images/visualizing-marker-genes_21_0.png

Trajectory inference

Get started with the following example for hematopoiesis for data of [Paul15]: → tutorial: paga-paul15

http://www.falexwolf.de/img/paga_paul15.png

More examples for trajectory inference on complex datasets can be found in the PAGA repository [Wolf19], for instance, multi-resolution analyses of whole animals, such as for planaria for data of [Plass18].

http://www.falexwolf.de/img/paga_planaria.png

As a reference for simple pseudotime analyses, we provide the diffusion pseudotime (DPT) analyses of [Haghverdi16] for two hematopoiesis datasets: DPT example 1 [Paul15] and DPT example 2 [Moignard15].

Integrating datasets

Map labels and embeddings of reference data to new data: → tutorial: integrating-data-using-ingest

https://scanpy-tutorials.readthedocs.io/en/latest/_images/integrating-data-using-ingest_21_0.png

Further Tutorials

Conversion: AnnData, SingleCellExperiment, and Seurat objects

See the Seurat to AnnData notebook for a tutorial on anndata2ri.

Regressing out cell cycle

See the cell cycle notebook.

Scaling Computations

http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/tsne_1.3M.png

Visualize and cluster 1.3M neurons from 10x Genomics.

Simulations

Simulating single cells using literature-curated gene regulatory networks [Wittmann09].

http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/timeseries.png http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/draw_graph.png

Images

See pseudotime-time inference on deep-learning based features for cell cycle reconstruction from image data [Eulenberg17].