scCross: A Deep Generative Model for Unifying Single-cell Multi-omics with Seamless Integration, Cross-modal Generation, and In-silico Exploration
Author:
Yang Xiuhui, Mann Koren K., Wu HaoORCID, Ding JunORCID
Abstract
AbstractSingle-cell multi-omics illuminate intricate cellular states, yielding transformative insights into cellular dynamics and disease. Yet, while the potential of this technology is vast, the integration of its multifaceted data presents challenges. Some modalities have not reached the robustness or clarity of established scRNA-seq. Coupled with data scarcity for newer modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross: a tool adeptly engineered using variational autoencoder, generative adversarial network principles, and the Mutual Nearest Neighbors (MNN) technique for modality alignment. This synergy ensures seamless integration of varied single-cell multi-omics data. Beyond its foundational prowess in multi-omics data integration, scCross excels in single-cell cross-modal data generation, multi-omics data simulation, and profound in-silico cellular perturbations. Armed with these capabilities, scCross is set to transform the field of single-cell research, establishing itself in the nuanced integration, generation, and simulation of complex multi-omics data.
Publisher
Cold Spring Harbor Laboratory
Reference85 articles.
1. Xue, R. , Zhang, Q. , Cao, Q. , Kong, R. , Xiang, X. , Liu, H. , Feng, M. , Wang, F. , Cheng, J. , Li, Z. , et al.: Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature, 1–7 (2022) 2. Blanchard, J.W. , Akay, L.A. , Davila-Velderrain, J. , von Maydell, D. , Mathys, H. , Davidson, S.M. , Effenberger, A. , Chen, C.-Y. , Maner-Smith, K. , Hajjar, I. , et al.: Apoe4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Nature, 1–11 (2022) 3. Niño, J.L.G. , Wu, H. , LaCourse, K.D. , Kempchinsky, A.G. , Baryiames, A. , Barber, B. , Futran, N. , Houlton, J. , Sather, C. , Sicinska, E. , et al.: Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature, 1–8 (2022) 4. Single-cell atac-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition;Cell Reports,2022 5. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells
|
|