References

BLP+20

Volker Bergen, Marius Lange, Stefan Peidli, F. Alexander Wolf, and Fabian J. Theis. Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology, 38(12):1408–1414, August 2020. URL: https://doi.org/10.1038/s41587-020-0591-3, doi:10.1038/s41587-020-0591-3.

GWL+23

Adam Gayoso, Philipp Weiler, Mohammad Lotfollahi, Dominik Klein, Justin Hong, Aaron Streets, Fabian J. Theis, and Nir Yosef. Deep generative modeling of transcriptional dynamics for rna velocity analysis in single cells. Nature Methods, September 2023. URL: http://dx.doi.org/10.1038/s41592-023-01994-w, doi:10.1038/s41592-023-01994-w.

MSZ+18

Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E. Kastriti, Peter Lönnerberg, Alessandro Furlan, Jean Fan, Lars E. Borm, Zehua Liu, David van Bruggen, Jimin Guo, Xiaoling He, Roger Barker, Erik Sundström, Gonçalo Castelo-Branco, Patrick Cramer, Igor Adameyko, Sten Linnarsson, and Peter V. Kharchenko. RNA velocity of single cells. Nature, 560(7719):494–498, August 2018. URL: https://doi.org/10.1038/s41586-018-0414-6, doi:10.1038/s41586-018-0414-6.

WLK+23

missing journal in Weiler2023

WAT18

F. Alexander Wolf, Philipp Angerer, and Fabian J. Theis. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology, February 2018. URL: https://doi.org/10.1186/s13059-017-1382-0, doi:10.1186/s13059-017-1382-0.

WHP+19

F. Alexander Wolf, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, and Fabian J. Theis. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology, March 2019. URL: https://doi.org/10.1186/s13059-019-1663-x, doi:10.1186/s13059-019-1663-x.