Package: miloR
Type: Package
Title: Differential neighbourhood abundance testing on a graph
Version: 2.9.1
Authors@R: 
    c(person("Mike", "Morgan", role=c("aut", "cre"), email="michael.morgan@abdn.ac.uk",
     comment=c(ORCID="0000-0003-0757-0711")),
    person("Emma", "Dann", role=c("aut", "ctb"), email="ed6@sanger.ac.uk"))
Description: 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.
License: GPL-3 + file LICENSE
Encoding: UTF-8
URL: https://marionilab.github.io/miloR
BugReports: https://github.com/MarioniLab/miloR/issues
biocViews: SingleCell, MultipleComparison, FunctionalGenomics, Software
LinkingTo: Rcpp, RcppArmadillo
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
Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown,
        uwot, scuttle, BiocStyle, MouseGastrulationData,
        MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq,
        graphics, sparseMatrixStats
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2026-06-23 16:14:52 UTC; root
Collate: 'AllClasses.R' 'AllGenerics.R' 'buildFromAdjacency.R'
        'buildGraph.R' 'calcNhoodExpression.R' 'calcNhoodDistance.R'
        'checkSeparation.R' 'countCells.R' 'findNhoodMarkers.R'
        'graphSpatialFDR.R' 'glmm.R' 'makeNhoods.R' 'milo.R'
        'miloR-package.R' 'methods.R' 'plotNhoods.R' 'sim_discrete.R'
        'sim_family.R' 'sim_nbglmm.R' 'sim_trajectory.R' 'testNhoods.R'
        'testDiffExp.R' 'utils.R' 'buildNhoodGraph.R'
        'annotateNhoods.R' 'groupNhoods.R' 'findNhoodGroupMarkers.R'
        'RcppExports.R' 'miloR.R'
VignetteBuilder: knitr
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-11 21:26:50 UTC
RemoteUrl: https://github.com/bioc/miloR
RemoteRef: HEAD
RemoteSha: ff744bbb5d793163b59f28483c1ad05192fddc15
Author: Mike Morgan [aut, cre] (ORCID: <https://orcid.org/0000-0003-0757-0711>),
  Emma Dann [aut, ctb]
Maintainer: Mike Morgan <michael.morgan@abdn.ac.uk>