Package: concordexR
Title: Identify Spatial Homogeneous Regions with concordex
Version: 1.13.0
Authors@R: c(
    person("Kayla", "Jackson", , "kaylajac@caltech.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-6483-0108")),
    person("A. Sina", "Booeshaghi", , "alisina@caltech.edu", role = "aut",
           comment = c(ORCID = "0000-0002-6442-4502")),
    person("Angel", "Galvez-Merchan", , "agalvezm@caltech.edu", role = "aut",
           comment = c(ORCID = "0000-0001-7420-8697")),
    person("Lambda", "Moses", , "dlu2@caltech.edu", role = "aut",
           comment = c(ORCID = "0000-0002-7092-9427")),
    person("Alexandra", "Kim", , "alexandrasuriya@gmail.com", role = "ctb"),
    person("Laura", "Luebbert", , "lauraluebbert@caltech.edu", role = "ctb",
           comment = c(ORCID = "0000-0003-1379-2927")),
    person("Lior", "Pachter", , "lpachter@caltech.edu", role = c("aut", "rev", "ths"),
           comment = c(ORCID = "0000-0002-9164-6231"))
  )
Description: Spatial homogeneous regions (SHRs) in tissues are domains
        that are homogenous with respect to cell type composition. We
        present a method for identifying SHRs using spatial
        transcriptomics data, and demonstrate that it is efficient and
        effective at finding SHRs for a wide variety of tissue types.
        concordex relies on analysis of k-nearest-neighbor (kNN)
        graphs. The tool is also useful for analysis of non-spatial
        transcriptomics data, and can elucidate the extent of
        concordance between partitions of cells derived from clustering
        algorithms, and transcriptomic similarity as represented in kNN
        graphs.
License: Artistic-2.0
URL: https://github.com/pachterlab/concordexR,
        https://pachterlab.github.io/concordexR/
BugReports: https://github.com/pachterlab/concordexR/issues
Depends: R (>= 4.5.0)
Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli,
        DelayedArray, Matrix, methods, purrr, rlang,
        SingleCellExperiment, sparseMatrixStats, SpatialExperiment,
        SummarizedExperiment
Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans,
        patchwork, rmarkdown, scater, SFEData,
        SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: SingleCell, Clustering, Spatial, Transcriptomics
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/pak/sysreqs: libglpk-dev libmagick++-dev gsfonts libicu-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:00:35 UTC
RemoteUrl: https://github.com/bioc/concordexR
RemoteRef: HEAD
RemoteSha: 3b93bdfd7a224aee10649d0e880910ba84fd332e
NeedsCompilation: no
Packaged: 2026-05-30 08:51:02 UTC; root
Author: Kayla Jackson [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6483-0108>),
  A. Sina Booeshaghi [aut] (ORCID:
    <https://orcid.org/0000-0002-6442-4502>),
  Angel Galvez-Merchan [aut] (ORCID:
    <https://orcid.org/0000-0001-7420-8697>),
  Lambda Moses [aut] (ORCID: <https://orcid.org/0000-0002-7092-9427>),
  Alexandra Kim [ctb],
  Laura Luebbert [ctb] (ORCID: <https://orcid.org/0000-0003-1379-2927>),
  Lior Pachter [aut, rev, ths] (ORCID:
    <https://orcid.org/0000-0002-9164-6231>)
Maintainer: Kayla Jackson <kaylajac@caltech.edu>