DOI: 10.18129/B9.bioc.miloR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see miloR.

Differential neighbourhood abundance testing on a graph

Bioconductor version: 3.16

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>

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HTML R Script 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
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biocViews FunctionalGenomics, MultipleComparison, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Suggests testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics
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