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Differential neighbourhood abundance testing on a graph

Bioconductor version: Release (3.18)

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.

Author: Mike Morgan [aut, cre], Emma Dann [aut, ctb]

Maintainer: Mike Morgan <michael.morgan at>

Citation (from within R, enter citation("miloR")):


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Differential abundance testing with Milo HTML R Script
Differential abundance testing with Milo - Mouse gastrulation example HTML R Script
Using contrasts for differential abundance testing HTML R Script
Reference Manual PDF


biocViews FunctionalGenomics, MultipleComparison, SingleCell, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0.0), edgeR
Imports BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices
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Suggests testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics
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