References

References#

[AAB+20]

Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, and Oliver Stegle. Mofa+: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biology, 2020. doi:10.1186/s13059-020-02015-1.

[ABM+22]

Erick Armingol, Hratch M. Baghdassarian, Cameron Martino, Araceli Perez-Lopez, Caitlin Aamodt, Rob Knight, and Nathan E. Lewis. Context-aware deconvolution of cell–cell communication with tensor-cell2cell. Nature Communications, 2022. doi:10.1038/s41467-022-31369-2.

[BiMVSB+22]

Pau Badia-i-Mompel, Jesús Vélez Santiago, Jana Braunger, Celina Geiss, Daniel Dimitrov, Sophia Müller-Dott, Petr Taus, Aurelien Dugourd, Christian H Holland, Ricardo O Ramirez Flores, and Julio Saez-Rodriguez. Decoupler: ensemble of computational methods to infer biological activities from omics data. Bioinformatics Advances, 2022. doi:10.1093/bioadv/vbac016.

[BKS22]

Danila Bredikhin, Ilia Kats, and Oliver Stegle. Muon: multimodal omics analysis framework. Genome Biology, 2022. doi:10.1186/s13059-021-02577-8.

[DSF+24]

Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, and Julio Saez-Rodriguez. Liana+ provides an all-in-one framework for cell–cell communication inference. Nature Cell Biology, 26(9):1613–1622, 2024. doi:10.1038/s41556-024-01469-w.

[DTGR+22]

Daniel Dimitrov, Dénes Türei, Martin Garrido-Rodriguez, Paul L. Burmedi, James S. Nagai, Charlotte Boys, Ricardo O. Ramirez Flores, Hyojin Kim, Bence Szalai, Ivan G. Costa, Alberto Valdeolivas, Aurélien Dugourd, and Julio Saez-Rodriguez. Comparison of methods and resources for cell-cell communication inference from single-cell rna-seq data. Nature Communications, 2022. doi:10.1038/s41467-022-30755-0.

[PSK+22]

Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, and Fabian J. Theis. Squidpy: a scalable framework for spatial omics analysis. Nature Methods, 19(2):171–178, 2022. doi:10.1038/s41592-021-01358-2.

[TFG+22]

Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro, and Julio Saez-Rodriguez. Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. Genome Biology, 2022. doi:10.1186/s13059-022-02663-5.

[TVG+21]

Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio‐Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian Theis, Dezső Módos, Tamás Korcsmáros, and Julio Saez‐Rodriguez. Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis. Molecular Systems Biology, 2021. doi:10.15252/msb.20209923.

[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.

[VRT+24]

Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, and F. Alexander Wolf. Anndata: access and store annotated data matrices. Journal of Open Source Software, 9(101):4371, 2024. doi:10.21105/joss.04371.

[WAT18]

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