The most recent version of the book is rendered here.

This book builds upon our expert recommendation "Best practices for single-cell analysis across modalities": https://www.nature.com/articles/s41576-023-00586-w. If you found the expert recommendation or this book helpful for your research article please cite it as:

Heumos, L., Schaar, A.C., Lance, C. et al. Best practices for single-cell analysis across modalities. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00586-w

We are writing a book on the current single-cell analysis best-practices with extensive tutorials and code examples.

We would like to invite the community to further improve the tutorial and the teaching material. Please read contributing for further instructions.

In case of questions or problems, please get in touch by posting an issue in this repository.

All notebooks for the various steps can be found in the jupyter book folder together with minimal Conda environments. Alternatively, the notebooks can be downloaded directly from the rendered version.

This tutorial would not be possible without the input of all Theislab members and the countless benchmarks and reviews of various single-cell tools by the community.