miloR

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see miloR.

Differential neighbourhood abundance testing on a graph

Bioconductor version: 3.13

This package 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>

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

Installation

To install this package, start R (version "4.1") and enter:


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

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("miloR")

Differential abundance testing with Milo HTML R Script

Differential abundance testing with Milo - Mouse gastrulation example HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FunctionalGenomics, MultipleComparison, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

License GPL-3 + file LICENSE

Depends R (>= 4.0.0), edgeR

Imports BiocNeighbors, 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

System Requirements

URL https://marionilab.github.io/miloR

Bug Reports https://github.com/MarioniLab/miloR/issues

Suggests testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, BiocStyle, MouseGastrulationData, magick, RCurl, curl, graphics

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