Current best practices in single‐cell RNA‐seq analysis: a tutorial von Luecken, Malte D, Theis, Fabian J

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Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape von Zappia, Luke, Theis, Fabian J

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SCANPY: large-scale single-cell gene expression data analysis von Wolf, F Alexander, Angerer, Philipp, Theis, Fabian J

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Diffusion maps for high-dimensional single-cell analysis of differentiation data von Haghverdi, Laleh, Buettner, Florian, Theis, Fabian J

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Generalizing RNA velocity to transient cell states through dynamical modeling von Bergen, Volker, Lange, Marius, Peidli, Stefan, Wolf, F. Alexander, Theis, Fabian J.

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Single-cell RNA-seq denoising using a deep count autoencoder von Eraslan, Gökcen, Simon, Lukas M., Mircea, Maria, Mueller, Nikola S., Theis, Fabian J.

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Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks von Fröhlich, Fabian, Kaltenbacher, Barbara, Theis, Fabian J, Hasenauer, Jan

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Spatial components of molecular tissue biology von Palla, Giovanni, Fischer, David S., Regev, Aviv, Theis, Fabian J.

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A test metric for assessing single-cell RNA-seq batch correction von Büttner, Maren, Miao, Zhichao, Wolf, F. Alexander, Teichmann, Sarah A., Theis, Fabian J.

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destiny: diffusion maps for large-scale single-cell data in R von Angerer, Philipp, Haghverdi, Laleh, Büttner, Maren, Theis, Fabian J, Marr, Carsten, Buettner, Florian

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PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells von Wolf, F Alexander, Hamey, Fiona K, Plass, Mireya, Solana, Jordi, Dahlin, Joakim S, Göttgens, Berthold, Rajewsky, Nikolaus, Simon, Lukas, Theis, Fabian J

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CellRank for directed single-cell fate mapping von Lange, Marius, Bergen, Volker, Klein, Michal, Setty, Manu, Reuter, Bernhard, Bakhti, Mostafa, Lickert, Heiko, Ansari, Meshal, Schniering, Janine, Schiller, Herbert B., Pe’er, Dana, Theis, Fabian J.

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Squidpy: a scalable framework for spatial omics analysis von Palla, Giovanni, Spitzer, Hannah, Klein, Michal, Fischer, David, Schaar, Anna Christina, Kuemmerle, Louis Benedikt, Rybakov, Sergei, Ibarra, Ignacio L., Holmberg, Olle, Virshup, Isaac, Lotfollahi, Mohammad, Richter, Sabrina, Theis, Fabian J.

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Benchmarking atlas-level data integration in single-cell genomics von Luecken, Malte D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., Theis, Fabian J.

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RNA velocity—current challenges and future perspectives von Bergen, Volker, Soldatov, Ruslan A, Kharchenko, Peter V, Theis, Fabian J

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Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation von Brunner, Andreas‐David, Thielert, Marvin, Vasilopoulou, Catherine, Ammar, Constantin, Coscia, Fabian, Mund, Andreas, Hoerning, Ole B, Bache, Nicolai, Apalategui, Amalia, Lubeck, Markus, Richter, Sabrina, Fischer, David S, Raether, Oliver, Park, Melvin A, Meier, Florian, Theis, Fabian J, Mann, Matthias

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A BaSiC tool for background and shading correction of optical microscopy images von Peng, Tingying, Thorn, Kurt, Schroeder, Timm, Wang, Lichao, Theis, Fabian J., Marr, Carsten, Navab, Nassir

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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells von Buettner, Florian, Natarajan, Kedar N, Casale, F Paolo, Proserpio, Valentina, Scialdone, Antonio, Theis, Fabian J, Teichmann, Sarah A, Marioni, John C, Stegle, Oliver

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Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network von Krumsiek, Jan, Marr, Carsten, Schroeder, Timm, Theis, Fabian J

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Mapping single-cell data to reference atlases by transfer learning von Lotfollahi, Mohammad, Naghipourfar, Mohsen, Luecken, Malte D., Khajavi, Matin, Büttner, Maren, Wagenstetter, Marco, Avsec, Žiga, Gayoso, Adam, Yosef, Nir, Interlandi, Marta, Rybakov, Sergei, Misharin, Alexander V., Theis, Fabian J.

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