Package: concordexR
Title: Identify Spatial Homogeneous Regions with concordex
Version: 1.7.1
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 (>= 4.4.0)
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
git_url: https://git.bioconductor.org/packages/concordexR
git_branch: devel
git_last_commit: 82b99bd
git_last_commit_date: 2025-01-16
Repository: Bioconductor 3.21
Date/Publication: 2025-03-25
NeedsCompilation: no
Packaged: 2025-03-25 22:17:45 UTC; biocbuild
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>
Built: R 4.5.0; ; 2025-03-26 11:58:18 UTC; windows
