scvi-tools
single-cell variational inference tools
End-to-end analysis of single cell omics data with deep generative models.
Please check out the scvi-tools website, or help contribute on GitHub.
Relevant publications
Consensus prediction of cell type labels with popV
C. Ergen, G. Xing, C. Xu, M. Jayasuriya, E. McGeever, A.O. Pisco, A. Streets, N. Yosef
bioRxiv ,
10.1101/2023.08.18.553912
GitHub
bioRxiv preprint
C. Ergen, G. Xing, C. Xu, M. Jayasuriya, E. McGeever, A.O. Pisco, A. Streets, N. Yosef
bioRxiv ,
10.1101/2023.08.18.553912
GitHub
bioRxiv preprint
Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics
P. Boyeau*, J. Hong*, A. Gayoso, M. Kim, JL. McFaline-Figueroa, M. Jordan, E. Azizi, C. Ergen\†, N. Yosef\†
bioRxiv , 2024
10.1101/2022.10.04.510898
bioRxiv preprint
P. Boyeau*, J. Hong*, A. Gayoso, M. Kim, JL. McFaline-Figueroa, M. Jordan, E. Azizi, C. Ergen\†, N. Yosef\†
bioRxiv , 2024
10.1101/2022.10.04.510898
bioRxiv preprint
Calibrated Identification of Feature Dependencies in Single-cell Multiomics
P. Boyeau, S. Bates, C. Ergen, MI. Jordan, N. Yosef
bioRxiv , 2024
10.1101/2023.11.03.565520
bioRxiv preprint
P. Boyeau, S. Bates, C. Ergen, MI. Jordan, N. Yosef
bioRxiv , 2024
10.1101/2023.11.03.565520
bioRxiv preprint
Scvi-hub: an actionable repository for model-driven single cell analysis
C. Ergen, VV. Pour Amiri, M. Kim, A. Streets, A. Gayoso, N. Yosef
bioRxiv , 2024
10.1101/2024.03.01.582887
bioRxiv preprint
C. Ergen, VV. Pour Amiri, M. Kim, A. Streets, A. Gayoso, N. Yosef
bioRxiv , 2024
10.1101/2024.03.01.582887
bioRxiv preprint
AutoEval Done Right: Using Synthetic Data for Model Evaluation
P. Boyeau, AN. Angelopoulos, N. Yosef, J. Malik, MI. Jordan
arXiv , 2024
10.48550/arXiv.2403.07008
P. Boyeau, AN. Angelopoulos, N. Yosef, J. Malik, MI. Jordan
arXiv , 2024
10.48550/arXiv.2403.07008
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
A. Gayoso*, P. Weiler*, M. Lotfollahi, D. Klein, J. Hong, A. Streets, FJ. Theis†, N. Yosef†
Nature Methods , 2024
10.1038/s41592-023-01994-w
A. Gayoso*, P. Weiler*, M. Lotfollahi, D. Klein, J. Hong, A. Streets, FJ. Theis†, N. Yosef†
Nature Methods , 2024
10.1038/s41592-023-01994-w
An Empirical Bayes Method for Differential Expression Analysis of Single Cells with Deep Generative Models
P. Boyeau, J. Regier, A. Gayoso, M.I. Jordan, R. Lopez†, N. Yosef†
Proc Natl Acad Sci , 2023
10.1073/pnas.2209124120
P. Boyeau, J. Regier, A. Gayoso, M.I. Jordan, R. Lopez†, N. Yosef†
Proc Natl Acad Sci , 2023
10.1073/pnas.2209124120
MultiVI: deep generative model for the integration of multi-modal data.
T. Ashuach*, M. Gabitto*, M. Jordan, N. Yosef
Nature Methods , 2023
10.1038/s41592-023-01909-9
GitHub
T. Ashuach*, M. Gabitto*, M. Jordan, N. Yosef
Nature Methods , 2023
10.1038/s41592-023-01909-9
GitHub
The scverse project provides a computational ecosystem for single-cell omics data analysis
Virshup I*, Bredikhin D*, Heumos L*, Palla G*, Sturm G*, Gayoso A*, Kats I, Koutrouli M; Scverse Community; Berger B, Pe’er D, Regev A, Teichmann SA, Finotello F†, Wolf FA†, Yosef N†, Stegle O†, Theis FJ†
Nature Biotechnology , 2023
10.1038/s41587-023-01733-8
Virshup I*, Bredikhin D*, Heumos L*, Palla G*, Sturm G*, Gayoso A*, Kats I, Koutrouli M; Scverse Community; Berger B, Pe’er D, Regev A, Teichmann SA, Finotello F†, Wolf FA†, Yosef N†, Stegle O†, Theis FJ†
Nature Biotechnology , 2023
10.1038/s41587-023-01733-8
A Python library for probabilistic analysis of single-cell omics data.
A. Gayoso*, R. Lopez*, G. Xing*, P. Boyeau, V. Valiollah Pour Amiri, J. Hong, K. Wu, M. Jayasuriya, E. Melhman, M. Langevin, Y. Liu, J. Samaran, G. Misrachi, A. Nazaret, O. Clivio, C. Xu, T. Ashuach, M. Lotfollahi, V.Svensson, E. da Veiga Beltrame, V. Kleshchevnikov, C. Talavera-Lopez, L. Pachter, F.J. Theis, A. Streets, M.I. Jordan, J. Regier, N. Yosef
Nature Biotechnology , 2022
10.1038/s41587-021-01206-w
GitHub
bioRxiv preprint
A. Gayoso*, R. Lopez*, G. Xing*, P. Boyeau, V. Valiollah Pour Amiri, J. Hong, K. Wu, M. Jayasuriya, E. Melhman, M. Langevin, Y. Liu, J. Samaran, G. Misrachi, A. Nazaret, O. Clivio, C. Xu, T. Ashuach, M. Lotfollahi, V.Svensson, E. da Veiga Beltrame, V. Kleshchevnikov, C. Talavera-Lopez, L. Pachter, F.J. Theis, A. Streets, M.I. Jordan, J. Regier, N. Yosef
Nature Biotechnology , 2022
10.1038/s41587-021-01206-w
GitHub
bioRxiv preprint
DestVI identifies continuums of cell types in spatial transcriptomics data
R. Lopez*, B. Li*, H. Keren-Shaul*, P. Boyeau, M. Kedmi, D. Pilzer, A.Jelinski, E. David, A. Wagner, Y. Addadi, M.I. Jordan, I. Amit†, N. Yosef†
Nature Biotechnology , 2022
10.1038/s41587-022-01272-8
GitHub
R. Lopez*, B. Li*, H. Keren-Shaul*, P. Boyeau, M. Kedmi, D. Pilzer, A.Jelinski, E. David, A. Wagner, Y. Addadi, M.I. Jordan, I. Amit†, N. Yosef†
Nature Biotechnology , 2022
10.1038/s41587-022-01272-8
GitHub
PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis.
T. Ashuach, DA. Reidenbach, A. Gayoso, N. Yosef
Cell Reports Methods , 2022
10.1016/j.crmeth.2022.100182
GitHub
T. Ashuach, DA. Reidenbach, A. Gayoso, N. Yosef
Cell Reports Methods , 2022
10.1016/j.crmeth.2022.100182
GitHub
Joint probabilistic modeling of single-cell multi-omic data with totalVI.
A. Gayoso*, Z. Steier*, R. Lopez, J. Regier, KL. Nazor, A. Streets†, N Yosef†
Nature Methods , 2021
10.1038/s41592-020-01050-x
GitHub
bioRxiv preprint
Reproducibility code
A. Gayoso*, Z. Steier*, R. Lopez, J. Regier, KL. Nazor, A. Streets†, N Yosef†
Nature Methods , 2021
10.1038/s41592-020-01050-x
GitHub
bioRxiv preprint
Reproducibility code
Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data.
K. Ouardini, R. Lopez, MG. Jones, S. Prillo, R. Zhang, MI. Jordan, N. Yosef
ICML 2021 Workshop on Computational Biology , 2021
10.1101/2021.05.28.446021
GitHub
bioRxiv preprint
K. Ouardini, R. Lopez, MG. Jones, S. Prillo, R. Zhang, MI. Jordan, N. Yosef
ICML 2021 Workshop on Computational Biology , 2021
10.1101/2021.05.28.446021
GitHub
bioRxiv preprint
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
C. Xu*, R. Lopez*, E. Mehlman*, J. Regier, M.I. Jordan, N. Yosef
Molecular Systems Biology , 2020
10.15252/msb.20209620
GitHub
Reproducibility code
C. Xu*, R. Lopez*, E. Mehlman*, J. Regier, M.I. Jordan, N. Yosef
Molecular Systems Biology , 2020
10.15252/msb.20209620
GitHub
Reproducibility code
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements.
R. Lopez*, A. Nazaret*, M. Langevin*, J. Samaran*, J. Regier*, M.I. Jordan, N. Yosef
ICML 2019 Workshop on Computational Biology (spotlight presentation; best student’s poster) , 2019
arXiv preprint
Reproducibility code
R. Lopez*, A. Nazaret*, M. Langevin*, J. Samaran*, J. Regier*, M.I. Jordan, N. Yosef
ICML 2019 Workshop on Computational Biology (spotlight presentation; best student’s poster) , 2019
arXiv preprint
Reproducibility code
Deep generative models for detecting differential expression in single cells.
P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint
P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint
Detecting zero-inflated genes in single-cell transcriptomics data.
O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef
Machine Learning in Computational Biology meeting (spotlight presentation) , 2019
bioRxiv preprint
Reproducibility code
O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef
Machine Learning in Computational Biology meeting (spotlight presentation) , 2019
bioRxiv preprint
Reproducibility code
Deep generative modeling for single-cell transcriptomics.
R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef.
Nature Methods , 2018
10.1038/s41592-018-0229-2
GitHub
News and Views
R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef.
Nature Methods , 2018
10.1038/s41592-018-0229-2
GitHub
News and Views