Package: DenMark
Type: Package
Title: Cell-Density Correlated Genes from Spatial Transcriptomics
Version: 0.9.0
Authors@R: c(
    person("Mingchi", "Xu", role = "aut"),
    person(c("Alexandra", "M."), "Schmidt", role = "aut"),
    person("Qihuang", "Zhang", email = "qihuang.zhang@mcgill.ca",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1455-2159"))
  )
Description: Quantifies the dependence between local cell density and
        gene expression in single-cell resolution spatial
        transcriptomics data, such as data from the Xenium and MERFISH
        platforms. Cell locations form a point pattern and gene counts
        are its marks. After aggregation on a regular grid, cell counts
        and summed expression follow Poisson models driven by two
        coregionalized latent Gaussian fields with Matern covariance,
        approximated by Hilbert space basis functions; the correlation
        between the two fields measures the density-expression
        dependence. Models are fitted with 'Stan' through 'cmdstanr'.
        Functions cover the tissue boundary (an alpha shape of the
        cells), gridding, model fitting, posterior summaries,
        latent-field decomposition, spatial correlation ranges, and
        gene scans that call density-correlated genes.
License: MIT + file LICENSE
URL: https://stagill.github.io/DenMark/,
        https://github.com/StaGill/DenMark
BugReports: https://github.com/StaGill/DenMark/issues
Depends: R (>= 4.1.0)
Imports: cmdstanr (>= 0.5.0), posterior, ggplot2 (>= 3.4.0), rlang,
        stats, tools, utils
Suggests: future, future.apply, jsonlite, Matrix, patchwork,
        SeuratObject, sf, testthat (>= 3.0.0), knitr, rmarkdown
Remotes: stan-dev/cmdstanr
Additional_repositories: https://stan-dev.r-universe.dev
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.1
Repository: https://stagill.r-universe.dev
Date/Publication: 2026-10-25 20:18:38 UTC
RemoteUrl: https://github.com/StaGill/DenMark
RemoteRef: HEAD
RemoteSha: 99a1899a6b4b731ec18002580ccc6ca792c80f1e
NeedsCompilation: no
Packaged: 2026-10-25 22:52:15 UTC; root
Author: Mingchi Xu [aut],
  Alexandra M. Schmidt [aut],
  Qihuang Zhang [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1455-2159>)
Maintainer: Qihuang Zhang <qihuang.zhang@mcgill.ca>