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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.

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Visualization

This tutorial shows how to visually explore genes using scanpy. {tutorial}plotting/core

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Trajectory inference

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

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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].

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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

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Spatial data

  • Basic analysis of spatial data: {tutorial}spatial/basic-analysis
  • Integrating spatial data with scRNA-seq using scanorama: {tutorial}spatial/integration-scanorama
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Further Tutorials

(conversion-to-r)=

Conversion: AnnData, SingleCellExperiment, and Seurat objects

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Regressing out cell cycle

See the cell cycle notebook.

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Normalization with Pearson Residuals

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

Scaling Computations

Simulations

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

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Images

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

% User Examples % ~~~~~~~~~~~~~ % % January 12, 2018: Exploring the mouse cell atlas_ by David P. Cook. % Data by Tabula Muris Consortium. % % .. _Exploring the mouse cell atlas: https://github.com/dpcook/fun_analysis/blob/master/tabula_muris/mouse_atlas_scanpy.ipynb % .. _David P. Cook: https://twitter.com/DavidPCook % .. _Tabula Muris Consortium: https://www.biorxiv.org/content/early/2017/12/20/237446