Package: COMMOTR
Type: Package
Title: Screening Cell-Cell Communication in Spatial Transcriptomics via
        Collective Optimal Transport
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 = "0000-0002-0000-0000")),
    person("Zixian", "Cang", role = "ctb",
           comment = "Original Python COMMOT implementation"))
Description: Infers cell-cell communication in spatial transcriptomics
        data using collective optimal transport. The method models
        ligand-receptor interactions as optimal transport problems with
        spatial distance constraints, providing communication direction
        inference, cluster-level analysis, and comprehensive
        visualization. This is an R implementation based on the COMMOT
        algorithm (Cang et al., Nature Methods, 2023).
License: MIT + file LICENSE
URL: https://zaoqu-liu.github.io/COMMOTR/,
        https://github.com/Zaoqu-Liu/COMMOTR
BugReports: https://github.com/Zaoqu-Liu/COMMOTR/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews:
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.0), Matrix, methods, stats, Seurat (>= 4.0.0),
        SeuratObject, future, future.apply, ggplot2, igraph, dplyr,
        tidyr, scales, grDevices, rlang, RColorBrewer
LinkingTo: Rcpp, RcppArmadillo
Suggests: circlize, testthat (>= 3.0.0), knitr, rmarkdown, ggraph,
        tidygraph, viridis, patchwork
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: yes
SystemRequirements: C++11
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-24 19:36:13 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/COMMOTR
RemoteRef: main
RemoteSha: d201e5449329a215401be3f9d9b64410bfe5e669
Packaged: 2026-10-11 15:41:36 UTC; root
Author: Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0000-0000>),
  Zixian Cang [ctb] (Original Python COMMOT implementation)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>