miloR

This is the released version of miloR; for the devel version, see miloR.

Differential neighbourhood abundance testing on a graph

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DOI: 10.18129/B9.bioc.miloR

Bioconductor version: Release (3.22)

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

Author: Mike Morgan [aut, cre] ORCID iD ORCID: 0000-0003-0757-0711 , Emma Dann [aut, ctb]

Maintainer: Mike Morgan <michael.morgan at abdn.ac.uk>

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

Installation

To install this package, start R (version "4.5") 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

Mixed effect models for Milo DA testing HTML R Script

Using contrasts for differential abundance testing 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 2.6.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License GPL-3 + file LICENSE

Depends R (>= 4.0.0), edgeR

Imports BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv

System Requirements

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

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

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

Linking To Rcpp, RcppArmadillo, RcppEigen, RcppML

Enhances

Depends On Me

Imports Me dandelionR

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package miloR_2.6.0.tar.gz

Windows Binary (x86_64) miloR_2.5.1.zip

macOS Binary (x86_64) miloR_2.6.0.tgz

macOS Binary (arm64) miloR_2.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/miloR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miloR

Bioc Package Browser https://code.bioconductor.org/browse/miloR/

Package Short Url https://bioconductor.org/packages/miloR/

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