ArticleNature protocols2016
Visualization and cellular hierarchy inference of single-cell data using SPADE.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
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- IL-6R blockade combined with immunosuppressants alleviates adult-onset Still's disease through immune remodeling: a mass cytometry study.Journal of translational medicine · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology.Nature communications · 2023Article
- From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies.Briefings in bioinformatics · 2023Review
- Identifying dysregulated immune cell subsets following volumetric muscle loss with pseudo-time trajectories.Communications biology · 2023Article
- Analysis of cardiac single-cell RNA-sequencing data can be improved by the use of artificial-intelligence-based tools.Scientific reports · 2023Article
- Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data.Frontiers in immunology · 2023Article
- A Hashing-Based Framework for Enhancing Cluster Delineation of High-Dimensional Single-Cell Profiles.Phenomics (Cham, Switzerland) · 2022Article
- Chemical synthesis, biological activities and action on nuclear receptors of 20S(OH)DBioorganic chemistry · 2022Article
- Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures.Briefings in bioinformatics · 2022Article
- MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection.Nucleic acids research · 2022Article
- Microfluidics applications for high-throughput single cell sequencing.Journal of nanobiotechnology · 2021Review
- Modulating local S1P receptor signaling as a regenerative immunotherapy after volumetric muscle loss injury.Journal of biomedical materials research. Part A · 2021Article
- Human splenic myeloid derived suppressor cells: Phenotypic and clustering analysis.Cellular immunology · 2021Article
- IL-10 normalizes aberrant amygdala GABA transmission and reverses anxiety-like behavior and dependence-induced escalation of alcohol intake.Progress in neurobiology · 2021Article
- Local delivery of FTY720 induces neutrophil activation through chemokine signaling in an oronasal fistula model.Regenerative engineering and translational medicine · 2021Article
- Single-Cell Profiling of Kidney Transplant Recipients With Immunosuppressive Treatment Reveals the Dynamic Immune Characteristics.Frontiers in immunology · 2021Article
- Optimal Estimation of Wasserstein Distance on A Tree with An Application to Microbiome Studies.Journal of the American Statistical Association · 2021Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
High-throughput single-cell technologies provide an unprecedented view into cellular heterogeneity, yet they pose new challenges in data analysis and interpretation. In this protocol, we describe the use of Spanning-tree Progression Analysis of Density-normalized Events (SPADE), a density-based algorithm for visualizing single-cell data and enabling cellular hierarchy inference among subpopulations of similar cells. It was initially developed for flow and mass cytometry single-cell data. We describe SPADE's implementation and application using an open-source R package that runs on Mac OS X, Linux and Windows systems. A typical SPADE analysis on a 2.27-GHz processor laptop takes ∼5 min. We demonstrate the applicability of SPADE to single-cell RNA-seq data. We compare SPADE with recently developed single-cell visualization approaches based on the t-distribution stochastic neighborhood embedding (t-SNE) algorithm. We contrast the implementation and outputs of these methods for normal and malignant hematopoietic cells analyzed by mass cytometry and provide recommendations for appropriate use. Finally, we provide an integrative strategy that combines the strengths of t-SNE and SPADE to infer cellular hierarchy from high-dimensional single-cell data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.