ArticlePLoS computational biology2014
OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed.
- A Randomized, Double-Blinded, Placebo-Controlled, Phase 1 Study of a Replication-Defective Herpes Simplex Virus (HSV) Type 2 Vaccine, HSV529, in Adults With or Without HSV Infection.The Journal of infectious diseases · 2019Trial
- A Step-by-Step Guide to Successful Multiparametric Microbiota Flow Cytometry.Current protocols · 2026Article
- Bile acids mediate liver-bone marrow crosstalk.iScience · 2026Article
- Opsonization Improves Dual Proteomic Analysis ofJournal of proteome research · 2026Article
- The ligand preference of LRP1 is regulated by O-glycans.Science advances · 2026Article
- Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources.International journal of molecular sciences · 2026Review
- Article
- Optimisation and application of a T-cell antigen-specific activation assay as diagnostic and treatment-monitoring tool for tuberculosis.ERJ open research · 2026Article
- Automated cytotoxicity assessment of natural killer cells by flow cytometry.Frontiers in immunology · 2026Article
- Antisense transcription can induce expression memory via stable promoter repression.Genome biology · 2025Article
- cytoGPNet: Enhancing clinical outcome prediction accuracy using longitudinal cytometry data in small cohort studies.Patterns (New York, N.Y.) · 2025Article
- The DNA replication checkpoint targets the kinetochore to reposition DNA structure-induced replication damage to the nuclear periphery.Cell reports · 2025Article
- Automatic phenotyping using exhaustive projection pursuit.Communications biology · 2025Article
- Glow with the Flow: Reproducible Analysis of Transiently Transformed Protoplasts Using Dual Fluorescent Reporters in R.bioRxiv : the preprint server for biology · 2025Article
- Androgens inhibit protective CD8Nature communications · 2025Article
- SCPline: An interactive framework for the single-cell proteomics data preprocessing.Briefings in bioinformatics · 2025Article
- The response to anti-PD-1 and anti-LAG-3 checkpoint blockade is associated with regulatory T cell reprogramming.Science translational medicine · 2025Article
- Mechanisms of NLRP3 activation and inhibition elucidated by functional analysis of disease-associated variants.Nature immunology · 2025Article
- Multi-dimensional analysis of B cells reveals the expansion of memory and regulatory B-cell clusters in humans living in rural tropical areas.Clinical and experimental immunology · 2025Article
- Cord blood innate-like T cell responses in neonates born to healthy women and women living with HIV.Frontiers in immunology · 2025Article
63 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis framework designed to lower the barrier of entry to automated flow data analysis algorithms by addressing key areas that we believe have held back wider adoption of automated approaches. OpenCyto supports end-to-end data analysis that is robust and reproducible while generating results that are easy to interpret. We have improved the existing, widely used core BioConductor flow cytometry infrastructure by allowing analysis to scale in a memory efficient manner to the large flow data sets that arise in clinical trials, and integrating domain-specific knowledge as part of the pipeline through the hierarchical relationships among cell populations. Pipelines are defined through a text-based csv file, limiting the need to write data-specific code, and are data agnostic to simplify repetitive analysis for core facilities. We demonstrate how to analyze two large cytometry data sets: an intracellular cytokine staining (ICS) data set from a published HIV vaccine trial focused on detecting rare, antigen-specific T-cell populations, where we identify a new subset of CD8 T-cells with a vaccine-regimen specific response that could not be identified through manual analysis, and a CyTOF T-cell phenotyping data set where a large staining panel and many cell populations are a challenge for traditional analysis. The substantial improvements to the core BioConductor flow cytometry packages give OpenCyto the potential for wide adoption. It can rapidly leverage new developments in computational cytometry and facilitate reproducible analysis in a unified environment.
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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.