Package: miloR
Type: Package
Title: Differential neighbourhood abundance testing on a graph
Version: 1.8.1
Authors@R: 
    c(person("Mike", "Morgan", role=c("aut", "cre"), email="michael.morgan@abdn.ac.uk"),
    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 a 
    negative bionomial generalized linear 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
Depends: R (>= 4.0.0), edgeR
Imports: BiocNeighbors, BiocGenerics, 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
Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr,
        rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData,
        MouseThymusAgeing, magick, RCurl, curl, graphics
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2023-04-25 21:47:11 UTC; biocbuild
Collate: 'AllClasses.R' 'AllGenerics.R' 'buildFromAdjacency.R'
        'buildGraph.R' 'calcNhoodExpression.R' 'calcNhoodDistance.R'
        'countCells.R' 'findNhoodMarkers.R' 'graphSpatialFDR.R'
        'makeNhoods.R' 'milo.R' 'miloR-package.R' 'methods.R'
        'plotNhoods.R' 'sim_discrete.R' 'sim_trajectory.R'
        'testNhoods.R' 'testDiffExp.R' 'utils.R' 'buildNhoodGraph.R'
        'annotateNhoods.R' 'groupNhoods.R' 'findNhoodGroupMarkers.R'
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/miloR
git_branch: RELEASE_3_17
git_last_commit: 493ab6a
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Author: Mike Morgan [aut, cre],
  Emma Dann [aut, ctb]
Maintainer: Mike Morgan <michael.morgan@abdn.ac.uk>
Built: R 4.3.0; ; 2023-07-11 19:36:57 UTC; unix
