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 (3.14)

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 (!requireNamespace("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

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

browseVignettes("miloR")

 

HTML R Script Differential abundance testing with Milo
HTML R Script Differential abundance testing with Milo - Mouse gastrulation example
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews FunctionalGenomics, MultipleComparison, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
LinkingTo
Suggests testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, BiocStyle, MouseGastrulationData, magick, RCurl, curl, graphics
SystemRequirements
Enhances
URL https://marionilab.github.io/miloR
BugReports https://github.com/MarioniLab/miloR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package miloR_1.1.0.tar.gz
Windows Binary miloR_1.1.0.zip
macOS 10.13 (High Sierra) miloR_1.1.0.tgz
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

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