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Bioconductor - miloR (development version)

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 (3.22)

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: 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")

# 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")

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 Details biocViews FunctionalGenomics, MultipleComparison, SingleCell, Software Version 2.5.1 In Bioconductor since BioC 3.13 (R-4.1) (4 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 See More 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.

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