Package: miloR
Type: Package
Title: Differential neighbourhood abundance testing on a graph
Version: 2.5.1
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, RcppEigen, RcppML
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: 7.3.2
NeedsCompilation: yes
Packaged: 2025-06-05 00:46:24 UTC; biocbuild
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
git_url: https://git.bioconductor.org/packages/miloR
git_branch: devel
git_last_commit: 874ed1b
git_last_commit_date: 2025-06-04
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
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>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-06-05 13:24:33 UTC; windows
Archs: x64
