Tutorials

Clustering

For getting started, we recommend Scanpy’s reimplementation → tutorial: pbmc3k of Seurat’s [^cite_satija15] clustering tutorial for 3k PBMCs from 10x Genomics, containing preprocessing, clustering and the identification of cell types via known marker genes.

Visualization

This tutorial shows how to visually explore genes using scanpy. → tutorial: plotting/core

_images/stacked_violin_dotplot_matrixplot.png

Trajectory inference

Get started with the following example for hematopoiesis for data of [^cite_paul15]: → tutorial: paga-paul15

More examples for trajectory inference on complex datasets can be found in the PAGA repository [^cite_wolf19], for instance, multi-resolution analyses of whole animals, such as for planaria for data of [^cite_plass18].

As a reference for simple pseudotime analyses, we provide the diffusion pseudotime (DPT) analyses of [^cite_haghverdi16] for two hematopoiesis datasets: DPT example 1 [^cite_paul15] and DPT example 2 [^cite_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

Spatial data

Basic analysis of spatial data: → tutorial: spatial/basic-analysis
Integrating spatial data with scRNA-seq using scanorama: → tutorial: spatial/integration-scanorama

Further Tutorials

Conversion: AnnData, SingleCellExperiment, and Seurat objects

See Seurat to AnnData for a tutorial on anndata2ri.
See the Scanpy in R guide for a tutorial on interacting with Scanpy from R.

Regressing out cell cycle

See the cell cycle notebook.

Normalization with Pearson Residuals

Normalization of scRNA-seq data with Pearson Residuals, from [^cite_lause21]: → tutorial: tutorial_pearson_residuals

Scaling Computations

Visualize and cluster 1.3M neurons from 10x Genomics.

Simulations

Simulating single cells using literature-curated gene regulatory networks [^cite_wittmann09].

Notebook for myeloid differentiation
Notebook for simple toggleswitch

Images

See pseudotime-time inference on deep-learning based features for cell cycle reconstruction from image data [^cite_eulenberg17].