Evaluation of UMAP as an alternative to t-SNE for single-cell data
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Summary
Comment on the usefulness of UMAP high-dimensional cytometry and single-cell RNA sequencing, notably highlighting faster runtime and consistency, meaningful organization of cell clusters and preservation of continuums in UMAP compared to t-SNE.
- Type
- preprint
- Published
- 2018-04-10
- Cited by
- 53
- References
- 19
- Access
- Open access
- OpenAlex
- https://openalex.org/W2796897898
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:90992624
Keywords
Computer science, Consistency (knowledge bases), Projection (relational algebra), Dimensionality reduction, Curse of dimensionality
References
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- Visualizing Data using t-SNE
- Transcriptional Regulation of Mast Cell and Basophil Lineage Commitment
- Automated Mapping of Phenotype Space with Single-Cell Data
- Mass Cytometry of the Human Mucosal Immune System Identifies Tissue- and Disease-Associated Immune Subsets.
- Computational flow cytometry: helping to make sense of high-dimensional immunology data
- Haemopedia: An Expression Atlas of Murine Hematopoietic Cells
- A High-Dimensional Atlas of Human T Cell Diversity Reveals Tissue-Specific Trafficking and Cytokine Signatures.
- How to Use t-SNE Effectively
- SCENIC: Single-cell regulatory network inference and clustering
- UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
- Mapping the Mouse Cell Atlas by Microwell-Seq.
- UMAP: Uniform Manifold Approximation and Projection
Cited by
- Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
- UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
- PD-1 blockade partially recovers dysfunctional virus–specific B cells in chronic hepatitis B infection
- Dynamics of helper CD4 T cells during acute and stable allergic asthma
- Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry
- The art of using t-SNE for single-cell transcriptomics
- SHARP: Single-cell RNA-seq Hyper-fast and Accurate Processing via Ensemble Random Projection
- Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
- A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
- Single cell-derived spheroids capture the self-renewing subpopulations of metastatic ovarian cancer
- Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
- Organ-Specific Fate, Recruitment, and Refilling Dynamics of Tissue-Resident Macrophages during Blood-Stage Malaria.
- Beyond bulk: A review of single cell transcriptomics methodologies and applications
- A Bioinformatic Toolkit for Single-Cell mRNA Analysis.
- Multiplex MHC Class I Tetramer Combined with Intranuclear Staining by Mass Cytometry.
- Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming
- Development of circulating cell-free DNA reduced representation bisulfite sequencing for clinical methylomics diagnostics
- Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming
- Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses
- Single-cell RNA sequencing of adult Drosophila ovary identifies transcriptional programs governing oogenesis
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