dyngen: a multi-modal simulator for spearheading new single-cell omics analyses
Open accessPreprint — published as 10.1038/s41467-021-24152-2 · Paper page
Abstract
We present dyngen, a novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. We demonstrate its potential for spearheading novel computational methods on three novel applications: aligning cell developmental trajectories, single-cell regulatory network inference and estimation of RNA velocity.
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Cites
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Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
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Differential abundance testing on single-cell data using k-nearest neighbor graphs
Dann, E., Henderson, N. C., Teichmann, S. A., Morgan, M. D., & Marioni, J. C. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01033-z · Cited by 938 · see citing works
- Authors
- Cannoodt, R., Saelens, W., Deconinck, L., & Saeys, Y.
- Affiliations
- Ghent University (BE)
- Vlaams Instituut voor Biotechnologie (BE)
- Corresponding author
- Saeys, Yvan
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2020-02-06
- Volume
- 12
- Issue
- 1
- Pages
- 3942-3942
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8225657
- OpenAlex
- W3174608384
- Cited by
- 124
- References
- 3
- Citations by year
- 2026: 16 · 2025: 19 · 2024: 28 · 2023: 27 · 2022: 17 · 2021: 11 · 2020: 6
- FWCI
- 7.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Silicon Valley Community Foundation
- Chan Zuckerberg Initiative
- Vlaamse regering
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- single-cell simulation, regulatory network inference, RNA velocity, single-cell omics
- MeSH terms
- Algorithms, Computer Simulation, Computational Biology, Gene Expression Profiling, Gene Regulatory Networks, Single-Cell Analysis
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