Type: Package
Package: SpaceMarkers
Title: Spatial Interaction Markers
Version: 2.1.0
Authors@R: c(
    person(given = "Atul", family = "Deshpande", email = "adeshpande@jhu.edu", role = c("aut", "cre"), comment = c(ORCID="0000-0001-5144-6924")),
    person(given = "Ludmila", family = "Danilova", email = "ldanilo1@jhmi.edu", role = "ctb"),
    person(given = "Dmitrijs", family = "Lvovs", email = "dlvovs1@jh.edu", role = "ctb", comment = c(ORCID = "0009-0003-2152-6853"))
  )
BugReports: https://github.com/DeshpandeLab/SpaceMarkers/issues
URL: https://github.com/DeshpandeLab/SpaceMarkers
Description: Spatial transcriptomic technologies have helped to resolve the connection
            between gene expression and the 2D orientation of tissues relative to each other.
            However, the limited single-cell resolution makes it difficult to highlight the most 
            important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software,
            can help to find molecular interactions, by identifying genes associated with latent space 
            interactions in spatial transcriptomics.
Depends: 
    R (>= 4.4.0)
biocViews: SingleCell, GeneExpression, Software, Spatial, Transcriptomics
Imports:
    matrixStats,
    matrixTests,
    rstatix,
    spatstat.explore,
    spatstat.geom,
    ape,
    hdf5r,
    nanoparquet,
    jsonlite,
    Matrix,
    qvalue,
    stats,
    utils,
    methods,
    ggplot2,
    reshape2,
    RColorBrewer,
    circlize,
    mixtools,
    dplyr,
    readbitmap,
    rlang,
    effsize,
    viridis
Suggests: 
    data.table,
    devtools,
    knitr,
    cowplot,
    rjson,
    rmarkdown,
    BiocStyle,
    testthat (>= 3.0.0),
    CoGAPS,
    ComplexHeatmap
Enhances: 
    BiocParallel
VignetteBuilder: 
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
License: MIT + file LICENSE
git_url: https://git.bioconductor.org/packages/SpaceMarkers
git_branch: devel
git_last_commit: 2b359d8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
