ReviewNature protocols2021
Analyzing high-dimensional cytometry data using FlowSOM.
Review in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
106 citing papers in PubMed.
- A phase I/II trial of WT1-specific TCR gene therapy for patients with acute myeloid leukemia and active disease post-allogeneic hematopoietic cell transplantation: skewing towards NK-like phenotype impairs T cell function and persistence.Nature communications · 2025Trial
- In vitro Validation of a Novel Disposable Remover to Remove Activated Leukocytes Generated During Cardiopulmonary Bypass: A Pilot Study.Journal of inflammation research · 2025Trial
- Adjuvant dendritic cell-based immunotherapy after cytoreductive surgery and hyperthermic intraperitoneal chemotherapy in patients with malignant peritoneal mesothelioma: a phase II clinical trial.Journal for immunotherapy of cancer · 2023Trial
- Phenotypic profiling of neutrophils in acuteGut microbes · 2026Article
- Integrated single-cell multiomics reveals neutrophil-driven immune-metabolic reprogramming of Kupffer cells via thrombospondin-1/CD36 after surgical stress.JCI insight · 2026Article
- Patient-Derived Organoids as a Model to Understand Tumor Microenvironment-Driven Nano-Bio Interactions - A Framework Towards Improved Nanomedicine Translation.bioRxiv : the preprint server for biology · 2026Article
- Review
- Automated Computational Flow Cytometry Correlates Decreasing Neutrophil-to-Lymphocyte Ratio to Improved Survival in NSCLC after Immune Checkpoint Blockade.Cancer immunology research · 2026Article
- Integrated immune and endothelial profiling predicts 90-day mortality in postoperative sepsis and septic shock.EBioMedicine · 2026Observational
- HCV-specific CD4EBioMedicine · 2026Article
- Restoration of anti-bacterial innate immune cell function lags behind nutritional recovery among children convalescing from complicated severe acute malnutrition.Nature communications · 2026Article
- Signaling downstream of tumor-stroma interaction regulates mucinous colorectal adenocarcinoma apicobasal polarity.Nature communications · 2026Article
- B cell TET2 recruits OGT for nuclear TET2 and H2B O-GlcNAcylation to drive AID and BLIMP-1 expression and maturation of the antibody response.Cell reports · 2026Article
- Single-cell metabolic profiling of stallion spermatozoa by flow cytometry using NADH and FAD autofluorescence†.Biology of reproduction · 2026Article
- Mass cytometry reveals complex neutrophil heterogeneity in patients with severe sepsis.Intensive care medicine experimental · 2026Article
- Homeostatic mature dendritic cells instruct fibroblast specialization via Notch2 signaling to establish T cell niches.Immunity · 2026Article
- CD38 expression by neonatal human naive CD4+ T cells shapes their distinct metabolic and tolerogenic properties.The Journal of clinical investigation · 2026Article
- Protocol for generating high-quality, 45-color spectral flow cytometry data for unsupervised clustering to investigate aging in human PBMCs.STAR protocols · 2026Article
- Navigating the data processing for cytometry-based single-cell proteomics.Nature protocols · 2026Review
- Spatial proteomics in precision medicine: technologies, bioinformatics, and translational applications.Precision clinical medicine · 2026Review
46 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The dimensionality of cytometry data has strongly increased in the last decade, and in many situations the traditional manual downstream analysis becomes insufficient. The field is therefore slowly moving toward more automated approaches, and in this paper we describe the protocol for analyzing high-dimensional cytometry data using FlowSOM, a clustering and visualization algorithm based on a self-organizing map. FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and can help to gain deeper insights in fields such as immunology and oncology. Since the original FlowSOM publication (2015), we have validated the tool on a wide variety of datasets, and to write this protocol, we made use of this experience to improve the user-friendliness of the package (e.g., comprehensive functions replacing commonly required scripts). Where the original paper focused mainly on the algorithm description, this protocol offers user guidelines on how to implement the procedure, detailed parameter descriptions and troubleshooting recommendations. The protocol provides clearly annotated R code, and is therefore relevant for all scientists interested in computational high-dimensional analyses without requiring a strong bioinformatics background. We demonstrate the complete workflow, starting from data preparation (such as compensation, transformation and quality control), including detailed discussion of the different FlowSOM parameters and visualization options, and concluding with how the results can be further used to answer biological questions, such as statistical comparison between groups of interest. An average FlowSOM analysis takes 1-3 h to complete, though quality issues can increase this time considerably.
Indexed as
Identifiers
34172973What OpenQuestion holds
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.