ArticleNature communications2022
cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Automated and reproducible cell identification in mass cytometry using neural networks.Briefings in bioinformatics · 2023Pooled it
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- High-Dimensional Multimodal Data Integration for Immune-Driven Diseases: A Practical Guide.Methods in molecular biology (Clifton, N.J.) · 2027Article
- CytoVI: deep generative modeling of antibody-based single cell data.Nature methods · 2026Article
- CAR T-cell therapy as a definitive consolidation for older adults with B-ALL in first complete remission.Blood advances · 2026Article
- dioscRi enables transferable prediction of clinical outcomes in multi-parameter cytometry data.Nature communications · 2026Article
- Unsupervised Flow Cytometry Reveals a Constant Shift Towards Activated CD4Scandinavian journal of immunology · 2026Article
- Type I interferons enhance B cell activation and promote differentiation of double negative 2 cells in SLE.Lupus science & medicine · 2026Article
- BCL6 in T cells promotes type 1 diabetes by redirecting fates of insulin-autoreactive B lymphocytes.iScience · 2026Article
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- VoxelCoder: Classification of human cellular phenotypes via autoencoder batch alignment and hyperdimensional representation of cytometry data.Patterns (New York, N.Y.) · 2026Article
- CytoBatchFlagR: A Comprehensive Framework to Objectively Assess High-Parameter Cytometry Data for Batch Effects.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Peripheral Regulatory T Cells Display Dynamic Memory Subset Frequency and Inhibitory Marker Expression Across Pregnancy.American journal of reproductive immunology (New York, N.Y. : 1989) · 2026Article
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- Human Systems Immunology in the Omics Era: Challenges, Methods, and Emerging Directions.European journal of immunology · 2026Review
- NKG2A+ NK cell cytotoxicity of Epstein-Barr virus infected B cells is mediated through the NKG2D and NKp30 activating receptors.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- ImmunoPheno: A Computational Framework for Data-Driven Design and Analysis of Immunophenotyping Experiments.bioRxiv : the preprint server for biology · 2026Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Combining single-cell cytometry datasets increases the analytical flexibility and the statistical power of data analyses. However, in many cases the full potential of co-analyses is not reached due to technical variance between data from different experimental batches. Here, we present cyCombine, a method to robustly integrate cytometry data from different batches, experiments, or even different experimental techniques, such as CITE-seq, flow cytometry, and mass cytometry. We demonstrate that cyCombine maintains the biological variance and the structure of the data, while minimizing the technical variance between datasets. cyCombine does not require technical replicates across datasets, and computation time scales linearly with the number of cells, allowing for integration of massive datasets. Robust, accurate, and scalable integration of cytometry data enables integration of multiple datasets for primary data analyses and the validation of results using public datasets.
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