Type: Package
Package: SpaceMarkers
Title: Spatial Interaction Markers
Version: 2.3.1
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 = "Orian", family = "Stapleton", email = "ostaple1@jh.edu", role = "aut"),
    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: SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
        S4Vectors, 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, BiocFileCache, testthat (>= 3.0.0), CoGAPS,
        ComplexHeatmap, zellkonverter, anndataR
Enhances: BiocParallel
VignetteBuilder: knitr
Collate: 'AllClasses.R' 'AllGenerics.R' 'SpaceMarkers.R'
        'SpaceMarkersExperiment-methods.R' 'data.R'
        'findGenesOfInterest.R' 'getInteractingGenes.R'
        'getSpatialParameters.R' 'hdutils.R' 'plotLRCircos.R'
        'preprocessing.R' 'test-helper.R' 'utils.R'
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
License: MIT + file LICENSE
Config/pak/sysreqs: cmake make libhdf5-dev libmagick++-dev gsfonts
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-29 03:41:10 UTC
RemoteUrl: https://github.com/bioc/SpaceMarkers
RemoteRef: HEAD
RemoteSha: 145f3da779f89e7e4593c876911eb1c3c32e9287
NeedsCompilation: no
Packaged: 2026-06-08 07:18:29 UTC; root
Author: Atul Deshpande [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5144-6924>),
  Orian Stapleton [aut],
  Ludmila Danilova [ctb],
  Dmitrijs Lvovs [ctb] (ORCID: <https://orcid.org/0009-0003-2152-6853>)
Maintainer: Atul Deshpande <adeshpande@jhu.edu>