ArticleCytometry. Part A : the journal of the International Society for Analytical Cytology2017
Toward deterministic and semiautomated SPADE analysis.
Article in Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Multi-Dimensional Flow Cytometry Analyses Reveal a Dichotomous Role for Nitric Oxide in Melanoma Patients Receiving Immunotherapy.Frontiers in immunology · 2020Trial
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- Dissecting immunophenotypic diversity in multiple myeloma via mass cytometry: a call for harmonized gating strategies.Frontiers in immunology · 2025Review
- Assessment of Automated Flow Cytometry Data Analysis Tools within Cell and Gene Therapy Manufacturing.International journal of molecular sciences · 2022Article
- T lymphocyte and monocyte subsets are dysregulated in type 1 diabetes patients with peripheral neuropathic pain.Brain, behavior, & immunity - health · 2021Article
- Agile workflow for interactive analysis of mass cytometry data.Bioinformatics (Oxford, England) · 2021Article
- Dual delivery of IL-10 and AT-RvD1 from PEG hydrogels polarize immune cells towards pro-regenerative phenotypes.Biomaterials · 2021Article
- How to Prepare Spectral Flow Cytometry Datasets for High Dimensional Data Analysis: A Practical Workflow.Frontiers in immunology · 2021Article
- Mass Cytometry Defines Virus-Specific CD4ImmunoHorizons · 2020Article
- Risk-associated alterations in marrow T cells in pediatric leukemia.JCI insight · 2020Article
- A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2020Review
- VoPo leverages cellular heterogeneity for predictive modeling of single-cell data.Nature communications · 2020Article
- Slow progressors to type 1 diabetes lose islet autoantibodies over time, have few islet antigen-specific CD8Diabetologia · 2020Article
- Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data.Frontiers in cell and developmental biology · 2020Review
- Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2019Article
- Single-cell technologies in reproductive immunology.American journal of reproductive immunology (New York, N.Y. : 1989) · 2019Review
- Loss of CXCR3 expression on memory B cells in individuals with long-standing type 1 diabetes.Diabetologia · 2018Article
- Comparison of CyTOF assays across sites: Results of a six-center pilot study.Journal of immunological methods · 2018Article
- Immune Cell Profiling During Switching from Natalizumab to Fingolimod Reveals Differential Effects on Systemic Immune-Regulatory Networks and on Trafficking of Non-T Cell Populations into the Cerebrospinal Fluid-Results from the ToFingo Successor Study.Frontiers in immunology · 2018Article
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Abstract
SPADE stands for spanning-tree progression analysis for density-normalized events. It combines downsampling, clustering and a minimum-spanning tree to provide an intuitive visualization of high-dimensional single-cell data, which assists with the interpretation of the cellular heterogeneity underlying the data. SPADE has been widely used for analysis of high-content flow cytometry data and CyTOF data. The downsampling and clustering components of SPADE are both stochastic, which lead to stochasticity in the tree visualization it generates. Running SPADE twice on the same data may generate two different tree structures. Although they typically lead to the same biological interpretation of subpopulations present in the data, robustness of the algorithm can be improved. Another avenue of improvement is the interpretation of the SPADE tree, which involves visual inspection of multiple colored versions of the tree based on expression of measured markers. This is essentially manual gating on the SPADE tree and can benefit from automated algorithms. This article presents improvements of SPADE in both aspects above, leading to a deterministic SPADE algorithm and a software implementation for semiautomated interpretation. © 2017 International Society for Advancement of Cytometry.
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