# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "DenMark" in publications use:'
type: software
license: MIT
title: 'DenMark: Cell-Density Correlated Genes from Spatial Transcriptomics'
version: 0.9.0
doi: 10.64898/2026.04.02.713482
identifiers:
- type: doi
  value: 10.32614/CRAN.package.DenMark
abstract: 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.
authors:
- family-names: Xu
  given-names: Mingchi
- family-names: Schmidt
  given-names: Alexandra M.
- family-names: Zhang
  given-names: Qihuang
  email: qihuang.zhang@mcgill.ca
  orcid: https://orcid.org/0000-0003-1455-2159
preferred-citation:
  type: article
  title: 'DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated
    Genes from Spatial Transcriptomics'
  authors:
  - family-names: Xu
    given-names: Mingchi
  - family-names: Schmidt
    given-names: Alexandra M.
  - family-names: Zhang
    given-names: Qihuang
    orcid: https://orcid.org/0000-0003-1455-2159
    email: qihuang.zhang@mcgill.ca
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.04.02.713482
  url: https://doi.org/10.64898/2026.04.02.713482
  notes: Preprint; the revised manuscript is under review at Cell Reports Methods
repository: https://stagill.r-universe.dev
repository-code: https://github.com/StaGill/DenMark
commit: 99a1899a6b4b731ec18002580ccc6ca792c80f1e
url: https://stagill.github.io/DenMark/
date-released: '2026-10-25'
contact:
- family-names: Zhang
  given-names: Qihuang
  email: qihuang.zhang@mcgill.ca
  orcid: https://orcid.org/0000-0003-1455-2159
references:
- type: manual
  title: 'DenMark: Cell-Density Correlated Genes from Spatial Transcriptomics'
  authors:
  - family-names: Xu
    given-names: Mingchi
  - family-names: Schmidt
    given-names: Alexandra M.
  - family-names: Zhang
    given-names: Qihuang
    orcid: https://orcid.org/0000-0003-1455-2159
  year: '2026'
  notes: R package version 0.9.0
  url: https://github.com/StaGill/DenMark