| Squidpy: a scalable framework for spatial omics analysis G Palla, H Spitzer, M Klein, D Fischer, AC Schaar, LB Kuemmerle, ... Nature methods 19 (2), 171-178, 2022 | 600 | 2022 |
| Wnt addiction of genetically defined cancers reversed by PORCN inhibition B Madan, Z Ke, N Harmston, SY Ho, AO Frois, J Alam, DA Jeyaraj, ... Oncogene 35 (17), 2197-2207, 2016 | 358 | 2016 |
| anndata: Annotated data I Virshup, S Rybakov, FJ Theis, P Angerer, FA Wolf BioRxiv, 2021.12. 16.473007, 2021 | 171 | 2021 |
| The scverse project provides a computational ecosystem for single-cell omics data analysis I Virshup, D Bredikhin, L Heumos, G Palla, G Sturm, A Gayoso, I Kats, ... Nature biotechnology 41 (5), 604-606, 2023 | 136 | 2023 |
| Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish NI Bower, K Koltowska, C Pichol-Thievend, I Virshup, S Paterson, ... Nature neuroscience 20 (6), 774-783, 2017 | 105 | 2017 |
| The impact of APP on Alzheimer-like pathogenesis and gene expression in down syndrome iPSC-derived neurons DA Ovchinnikov, O Korn, I Virshup, CA Wells, EJ Wolvetang Stem cell reports 11 (1), 32-42, 2018 | 81 | 2018 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support J Moore, D Basurto-Lozada, S Besson, J Bogovic, J Bragantini, EM Brown, ... Histochemistry and Cell Biology 160 (3), 223-251, 2023 | 69 | 2023 |
| SpatialData: an open and universal data framework for spatial omics L Marconato, G Palla, KA Yamauchi, I Virshup, E Heidari, T Treis, ... Nature Methods, 1-5, 2024 | 54 | 2024 |
| Human CD141+ Dendritic Cell and CD1c+ Dendritic Cell Undergo Concordant Early Genetic Programming after Activation in Humanized Mice In Vivo Y Minoda, I Virshup, I Leal Rojas, O Haigh, Y Wong, JJ Miles, CA Wells, ... Frontiers in immunology 8, 1419, 2017 | 54 | 2017 |
| Alexander Wolf I Virshup, S Rybakov, FJ Theis, P Angerer F. anndata: Annotated data. bioRxiv 16, 2021, 2021 | 21 | 2021 |
| anndata: Access and store annotated data matrices I Virshup, S Rybakov, FJ Theis, P Angerer, FA Wolf Journal of Open Source Software 9 (101), 4371, 2024 | 15 | 2024 |
| numba/numba: Version 0.55. 0 SK Lam, A Pitrou, M Florisson, S Seibert, G Markall, TA Anderson, ... Zenodo, 2022 | 11 | 2022 |
| An open-source framework for end-to-end analysis of electronic health record data L Heumos, P Ehmele, T Treis, J Upmeier zu Belzen, E Roellin, L May, ... Nature medicine 30 (11), 3369-3380, 2024 | 5 | 2024 |
| Squidpy: a scalable framework for spatial single cell 2 analysis G Palla, H Spitzer, M Klein, D Fischer, A Christina, L Benedikt Kuemmerle, ... BioRxiv, 2021 | 5 | 2021 |
| Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data Y Wang, I Sarfraz, WK Teh, A Sokolov, BR Herb, HH Creasy, I Virshup, ... bioRxiv, 2023 | 4 | 2023 |
| numba/numba: 0.60. 0 SK Lam, A Pitrou, M Florisson, G Markall, S Seibert, E Self-Construct, ... Zenodo, 2024 | 3 | 2024 |
| numba/numba: Version 0.56. 4 SK Lam, A Pitrou, M Florisson, S Seibert, G Markall, TA Anderson, ... Zenodo, 2023 | 2 | 2023 |
| Exploratory electronic health record analysis with ehrapy L Heumos, P Ehmele, T Treis, J Upmeier zu Belzen, A Namsaraeva, ... medRxiv, 2023.12. 11.23299816, 2023 | 1 | 2023 |
| constclust: consistent clusters for scRNA-seq I Virshup, J Choi, KA Lê Cao, CA Wells bioRxiv, 2020.12. 08.417105, 2020 | 1 | 2020 |
| MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data I Sarfraz, Y Wang, A Shastry, WK Teh, A Sokolov, BR Herb, HH Creasy, ... Genome Biology 25 (1), 205, 2024 | | 2024 |
