Differential abundance testing on single-cell data using k-nearest neighbor graphs

Emma Dann, Neil C Henderson, Sarah A Teichmann, Michael D Morgan, John C Marioni

Research output: Contribution to journalArticlepeer-review


Current computational workflows for comparative analyses of single-cell datasets typically use discrete clusters as input when testing for differential abundance among experimental conditions. However, clusters do not always provide the appropriate resolution and cannot capture continuous trajectories. Here we present Milo, a scalable statistical framework that performs differential abundance testing by assigning cells to partially overlapping neighborhoods on a k-nearest neighbor graph. Using simulations and single-cell RNA sequencing (scRNA-seq) data, we show that Milo can identify perturbations that are obscured by discretizing cells into clusters, that it maintains false discovery rate control across batch effects and that it outperforms alternative differential abundance testing strategies. Milo identifies the decline of a fate-biased epithelial precursor in the aging mouse thymus and identifies perturbations to multiple lineages in human cirrhotic liver. As Milo is based on a cell-cell similarity structure, it might also be applicable to single-cell data other than scRNA-seq. Milo is provided as an open-source R software package at https://github.com/MarioniLab/miloR .

Original languageEnglish
Pages (from-to)245-253
Number of pages9
JournalNature Biotechnology
Issue number2
Early online date30 Sep 2021
Publication statusPublished - Feb 2022


  • Animals
  • Cluster Analysis
  • Gene Expression Profiling
  • Mice
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Software


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