ArticleNature methods2017
Testing for differential abundance in mass cytometry data.
Article in Nature methods, 2017. 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
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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.
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Who cites it
106 citing papers in PubMed.
- Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm.bioRxiv : the preprint server for biology · 2026Article
- Deciphering senescence-associated mechanisms through cell painting & transcriptomics.npj aging · 2026Article
- Differential Correlation Across Subpopulations of Single Cells in Subtypes of Acute Myeloid Leukemia.Biotech (Basel (Switzerland)) · 2026Article
- CytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.Nature genetics · 2026Article
- The automated computational workflow QUICHE reveals structural definitions of antitumor responses in triple-negative breast cancer.Nature cancer · 2026Article
- Single-cell differential abundance detection: A new angle on dissecting tumor heterogeneity.World journal of clinical oncology · 2026Review
- Ionizing radiation expands a p90RSK-activated patrolling monocyte subset: modulation by colchicine.Frontiers in cardiovascular medicine · 2026Article
- DiffHiChIP: Identifying differential chromatin contacts from HiChIP data.Cell reports methods · 2025Article
- CellPhenoX: An Explainable Machine Learning Method for Identifying Cell Phenotypes To Predict Clinical Outcomes from Single-Cell Multi-Omics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Kontextual reframes analysis of spatial omics data and reveals consistent cell relationships across images.Cell reports methods · 2025Article
- reDA: differential abundance testing on scATAC-seq data using random walk with restart.Bioinformatics (Oxford, England) · 2025Article
- Combined Flt3L and CD40 agonism restores dendritic cell-driven T cell immunity in pancreatic cancer.Science immunology · 2025Article
- Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy.The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation · 2025Article
- Single cell RNA sequencing of haematopoietic cells in fresh and frozen human atheroma tissue.Cardiovascular research · 2025Article
- Genetics- and age-driven neuroimmune and disc changes underscore herniation susceptibility and pain-associated behaviors in SM/J mice.Science advances · 2025Article
- Prolonged airway explant culture enables study of health, disease, and viral pathogenesis.Science advances · 2025Article
- Inhibition of CD226 co-stimulation suppresses diabetes development in the NOD mouse by augmenting regulatory T cells and diminishing effector T cell function.Diabetologia · 2025Article
- The aryl hydrocarbon receptor is associated with monocytic AML and innate immune resistance reversible with an AHR inhibitor.Frontiers in immunology · 2025Article
- Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating.Briefings in bioinformatics · 2024Article
- Trajectory-centric framework TrajAtlas reveals multi-scale differentiation heterogeneity among cells, genes, and gene modules in osteogenesis.PLoS genetics · 2024Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
When comparing biological conditions using mass cytometry data, a key challenge is to identify cellular populations that change in abundance. Here, we present a computational strategy for detecting 'differentially abundant' populations by assigning cells to hyperspheres, testing for significant differences between conditions and controlling the spatial false discovery rate. Our method (http://bioconductor.org/packages/cydar) outperforms other approaches in simulations and finds novel patterns of differential abundance in real 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.