References

References#

[ButtnerOMuller+21]

M. Büttner, J. Ostner, C. L. Müller, F. J. Theis, and B. Schubert. Sccoda is a bayesian model for compositional single-cell data analysis. Nature Communications, 12(1):6876, 2021. URL: https://doi.org/10.1038/s41467-021-27150-6, doi:10.1038/s41467-021-27150-6.

[DHT+22]

Emma Dann, Neil C. Henderson, Sarah A. Teichmann, Michael D. Morgan, and John C. Marioni. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nature Biotechnology, 40(2):245–253, 2022. URL: https://doi.org/10.1038/s41587-021-01033-z, doi:10.1038/s41587-021-01033-z.

[DWW+23]

Mingze Dong, Bao Wang, Jessica Wei, Antonio H. de O. Fonseca, Curtis J. Perry, Alexander Frey, Feriel Ouerghi, Ellen F. Foxman, Jeffrey J. Ishizuka, Rahul M. Dhodapkar, and David van Dijk. Causal identification of single-cell experimental perturbation effects with cinema-ot. Nature Methods, 20(11):1769–1779, 2023. URL: https://doi.org/10.1038/s41592-023-02040-5, doi:10.1038/s41592-023-02040-5.

[JAR22]

Livnat Jerby-Arnon and Aviv Regev. Dialogue maps multicellular programs in tissue from single-cell or spatial transcriptomics data. Nature Biotechnology, 40(10):1467–1477, 2022. URL: https://doi.org/10.1038/s41587-022-01288-0, doi:10.1038/s41587-022-01288-0.

[KCM+23]

Kazumasa Kanemaru, James Cranley, Daniele Muraro, Antonio M. A. Miranda, Siew Yen Ho, Anna Wilbrey-Clark, Jan Patrick Pett, Krzysztof Polanski, Laura Richardson, Monika Litvinukova, Natsuhiko Kumasaka, Yue Qin, Zuzanna Jablonska, Claudia I. Semprich, Lukas Mach, Monika Dabrowska, Nathan Richoz, Liam Bolt, Lira Mamanova, Rakeshlal Kapuge, Sam N. Barnett, Shani Perera, Carlos Talavera-López, Ilaria Mulas, Krishnaa T. Mahbubani, Liz Tuck, Lu Wang, Margaret M. Huang, Martin Prete, Sophie Pritchard, John Dark, Kourosh Saeb-Parsy, Minal Patel, Menna R. Clatworthy, Norbert Hübner, Rasheda A. Chowdhury, Michela Noseda, and Sarah A. Teichmann. Spatially resolved multiomics of human cardiac niches. Nature, 619(7971):801–810, 2023. URL: https://doi.org/10.1038/s41586-023-06311-1, doi:10.1038/s41586-023-06311-1.

[LWT19]

Mohammad Lotfollahi, F. Alexander Wolf, and Fabian J. Theis. Scgen predicts single-cell perturbation responses. Nature Methods, 16(8):715–721, 2019. URL: https://doi.org/10.1038/s41592-019-0494-8, doi:10.1038/s41592-019-0494-8.

[OCM21]

Johannes Ostner, Salomé Carcy, and Christian L. Müller. Tasccoda: bayesian tree-aggregated analysis of compositional amplicon and single-cell data. Frontiers in Genetics, 2021. URL: https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.766405, doi:10.3389/fgene.2021.766405.

[PMB+21]

Efthymia Papalexi, Eleni P. Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck, Hans-Hermann Wessels, Yuhan Hao, Bertrand Z. Yeung, Peter Smibert, and Rahul Satija. Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens. Nature Genetics, 53(3):322–331, 2021. URL: https://doi.org/10.1038/s41588-021-00778-2, doi:10.1038/s41588-021-00778-2.

[PGS+24]

Stefan Peidli, Tessa D. Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J. Schumacher, Jake P. Taylor-King, Debora S. Marks, Augustin Luna, Nils Blüthgen, and Chris Sander. Scperturb: harmonized single-cell perturbation data. Nature Methods, 21(3):531–540, 2024. URL: https://doi.org/10.1038/s41592-023-02144-y, doi:10.1038/s41592-023-02144-y.

[RSP+22]

Joseph M. Replogle, Reuben A. Saunders, Angela N. Pogson, Jeffrey A. Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J. Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L. Bonnar, Marco Jost, Thomas M. Norman, and Jonathan S. Weissman. Mapping information-rich genotype-phenotype landscapes with genome-scale perturb-seq. Cell, 185(14):2559–2575.e28, 2022. URL: https://doi.org/10.1016/j.cell.2022.05.013, doi:10.1016/j.cell.2022.05.013.

[SSK+21]

MA Skinnider, JW Squair, C Kathe, MA Anderson, M Gautier, KJE Matson, M Milano, TH Hutson, Q Barraud, AA Phillips, LJ Foster, G La Manno, AJ Levine, and G Courtine. Cell type prioritization in single-cell data. Nature Biotechnology, 39(1):30–34, 2021. URL: https://doi.org/10.1038/s41587-020-0605-1, doi:10.1038/s41587-020-0605-1.

[VBH+23]

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.