DESCRIPTION

Package: miloR
Type: Package
Title: Differential neighbourhood abundance testing on a graph
Version: 2.1.3
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
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2020-07-31 14:15:28 UTC; morgan02
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