Package: CytoSPACER
Type: Package
Title: Mapping Single-Cell Transcriptomes to Spatial Transcriptomics
        Data
Version: 1.0.0
Date: 2026-01-25
Authors@R: c(
    person("Zaoqu", "Liu", 
           email = "liuzaoqu@163.com", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-5623-6869")),
    person("CytoSPACE Team", role = "ctb",
           comment = "Original Python implementation"))
Description: CytoSPACER is an R implementation of CytoSPACE, a
        computational strategy for assigning single-cell transcriptomes
        to in situ spatial transcriptomics (ST) data. The method solves
        single cell/spot assignment by minimizing a correlation-based
        cost function through a linear programming-based optimization
        routine using the Jonker-Volgenant algorithm. This package
        provides high-performance implementations using Rcpp and
        supports parallel processing across all platforms.
License: MIT + file LICENSE
URL: https://zaoqu-liu.github.io/CytoSPACER/,
        https://github.com/Zaoqu-Liu/CytoSPACER
BugReports: https://github.com/Zaoqu-Liu/CytoSPACER/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.10), data.table (>= 1.14.0), Matrix (>= 1.5.0),
        future (>= 1.32.0), future.apply (>= 1.11.0), progressr (>=
        0.14.0), ggplot2 (>= 3.4.0), methods, stats, utils
Suggests: Seurat (>= 4.0.0), SeuratObject (>= 4.0.0), testthat (>=
        3.0.0), knitr, rmarkdown, viridis
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Config/testthat/edition: 3
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-24 18:51:37 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/CytoSPACER
RemoteRef: main
RemoteSha: 885560a47a2170304bac1c921277a4633ee7a2e0
NeedsCompilation: yes
Packaged: 2026-07-04 11:10:26 UTC; root
Author: Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-5623-6869>),
  CytoSPACE Team [ctb] (Original Python implementation)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>