Package: scider
Type: Package
Title: Spatial cell-type inter-correlation by density in R
Version: 1.11.0
Authors@R: 
    c(person(given = "Mengbo",family = "Li", 
             role = c("aut"),
             email = "li.me@wehi.edu.au",
             comment = c(ORCID = "0000-0002-9666-5810")),
      person(given = "Ning", 
             family = "Liu",
             role = c("aut"),
             email = "liu.n@wehi.edu.au",
             comment = c(ORCID = "0000-0002-9487-9305")),
      person(given = "Quoc Hoang",
             family = "Nguyen",
             role = c("aut"),
             email = "nguyen.q@wehi.edu.au",
             comment = c(ORCID = "0009-0007-2828-7567")),
      person(given = "Yunshun",
             family = "Chen",
             role = c("aut", "cre"),
             email = "yuchen@wehi.edu.au",
             comment = c(ORCID = "0000-0003-4911-5653")))
Author: Mengbo Li, Ning Liu, Quoc Hoang Nguyen, Yunshun Chen
Maintainer: Yunshun Chen <yuchen@wehi.edu.au>
Description: scider is an user-friendly R package providing functions
        to model the global density of cells in a slide of spatial
        transcriptomics data. All functions in the package are built
        based on the SpatialExperiment object, allowing integration
        into various spatial transcriptomics-related packages from
        Bioconductor. After modelling density, the package allows for
        several downstream analysis, including colocalization analysis,
        boundary detection analysis and differential density analysis.
biocViews: Spatial, Transcriptomics
License: GPL-3 + file LICENSE
URL: https://github.com/ChenLaboratory/scider,
        https://chenlaboratory.github.io/scider/
BugReports: https://github.com/ChenLaboratory/scider/issues
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom,
        spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats,
        pheatmap, plotly, shiny, igraph, janitor, knitr, methods,
        utils, isoband, S4Vectors, grDevices, dbscan, hexDensity,
        hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba,
        DropletUtils, arrow, RBioFormats, Matrix
Suggests: edgeR, testthat (>= 3.0.0)
Config/testthat/edition: 3
Depends: R (>= 4.3)
VignetteBuilder: knitr
Config/pak/sysreqs: libabsl-dev cmake libfftw3-dev libgdal-dev gdal-bin
        libgeos-dev libglpk-dev make libmagick++-dev gsfonts
        default-jdk libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libxml2-dev libssl-dev libproj-dev libsqlite3-dev
        libudunits2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:01:50 UTC
RemoteUrl: https://github.com/bioc/scider
RemoteRef: HEAD
RemoteSha: 7dcb837f327cfc8ac9f649491c61c04c5e5be2e7
NeedsCompilation: yes
Packaged: 2026-07-04 22:10:28 UTC; root