Single-cell best practices

The most recent version of the book is rendered here.

Looking for help and maintainers

We are looking for help in maintaining the book. There are lots of open tasks for both newcomers and seasoned analysts.

Accompanying expert recommendation and citation

This book builds upon our expert recommendation Best practices for single-cell analysis across modalities. If you found the expert recommendation or this book helpful for your research article please cite it as:

@article{Heumos2023,
  author = {Heumos, Lukas and Schaar, Anna C. and Lance, Christopher and Litinetskaya, Anastasia and Drost, Felix and Zappia, Luke and Lücken, Malte D. and Strobl, Daniel C. and Henao, Juan and Curion, Fabiola and Aliee, Hananeh and Ansari, Meshal and Badia-i-Mompel, Pau and Büttner, Maren and Dann, Emma and Dimitrov, Daniel and Dony, Leander and Frishberg, Amit and He, Dongze and Hediyeh-zadeh, Soroor and Hetzel, Leon and Ibarra, Ignacio L. and Jones, Matthew G. and Lotfollahi, Mohammad and Martens, Laura D. and Müller, Christian L. and Nitzan, Mor and Ostner, Johannes and Palla, Giovanni and Patro, Rob and Piran, Zoe and Ramírez-Suástegui, Ciro and Saez-Rodriguez, Julio and Sarkar, Hirak and Schubert, Benjamin and Sikkema, Lisa and Srivastava, Avi and Tanevski, Jovan and Virshup, Isaac and Weiler, Philipp and Schiller, Herbert B. and Theis, Fabian J.},
  year = {2023},
  month = {03},
  title = {Best practices for single-cell analysis across modalities},
  journal = {Nature Reviews Genetics},
  volume = {24},
  number = {8},
  pages = {550--572},
  issn = {1471-0064},
  doi = {10.1038/s41576-023-00586-w},
  url = {https://doi.org/10.1038/s41576-023-00586-w}
}

Contributing

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.

Adapting the notebooks to other datasets

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.

Acknowledgements

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.