Package: miloR
Type: Package
Title: Differential neighbourhood abundance testing on a graph
Version: 1.0.0
Authors@R: 
    c(person("Mike", "Morgan", role=c("aut", "cre"), email="michael.morgan@cruk.cam.ac.uk"),
    person("Emma", "Dann", role=c("aut", "ctb"), email="ed6@sanger.ac.uk"))
Description: This package 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, 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, BiocStyle, MouseGastrulationData, magick,
        RCurl, curl, graphics
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2021-05-19 22:11:58 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_13
git_last_commit: 6e2750a
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
Author: Mike Morgan [aut, cre],
  Emma Dann [aut, ctb]
Maintainer: Mike Morgan <michael.morgan@cruk.cam.ac.uk>
Built: R 4.1.0; ; 2021-06-03 00:51:07 UTC; unix
