miloR

DOI: 10.18129/B9.bioc.miloR    

This is the development version of miloR; for the stable release version, see miloR.

Differential neighbourhood abundance testing on a graph

Bioconductor version: Development (3.17)

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 cruk.cam.ac.uk>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("miloR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	FunctionalGenomics, MultipleComparison, SingleCell, Software
Version	1.7.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 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
LinkingTo
Suggests	testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics
SystemRequirements
Enhances
URL	https://marionilab.github.io/miloR
BugReports	https://github.com/MarioniLab/miloR/issues
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/miloR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miloR
Package Short Url	https://bioconductor.org/packages/miloR/
Package Downloads Report	Download Stats