Package: SPIAT
Type: Package
Title: Spatial Image Analysis of Tissues
Version: 1.12.0
Authors@R: c(
    person(given = "Anna",
           family="Trigos",
           role=c("aut"),
           comment = c(ORCID = "0000-0002-5915-2952"),
           email="anna.trigos@petermac.org"),
    person(given = "Yuzhou",
           family = " Feng",
           role=c("aut", "cre"),
           comment = c(ORCID = "0000-0002-2955-4053"),
           email="yuzhou0610@gmail.com"),
    person(given = "Tianpei",
           family = " Yang",
           role="aut",
           email="yangtp3344@gmail.com"),
    person(given = "Mabel",
           family = " Li",
           role="aut"),
    person(given = "John",
           family = " Zhu",
           role="aut"),
    person(given = "Volkan",
           family=" Ozcoban",
           role="aut",
           email = "volkanozcoban1@gmail.com"),
    person(given = "Maria",
           family= "Doyle",
           role="aut",
           email = "maria.doyle@petermac.org"))
Description: SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues)
        is an R package with a suite of data processing, quality
        control, visualization and data analysis tools. SPIAT is
        compatible with data generated from single-cell spatial
        proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler).
        SPIAT reads spatial data in the form of X and Y coordinates of
        cells, marker intensities and cell phenotypes. SPIAT includes
        six analysis modules that allow visualization, calculation of
        cell colocalization, categorization of the immune
        microenvironment relative to tumor areas, analysis of cellular
        neighborhoods, and the quantification of spatial heterogeneity,
        providing a comprehensive toolkit for spatial data analysis.
License: Artistic-2.0 + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0)
Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3),
        gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN
        (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>=
        1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom,
        dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp,
        SummarizedExperiment, rlang
Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown,
        testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap,
        elsa
biocViews: BiomedicalInformatics, CellBiology, Spatial, Clustering,
        DataImport, ImmunoOncology, QualityControl, SingleCell,
        Software, Visualization
BugReports: https://github.com/trigosteam/SPIAT/issues
RoxygenNote: 7.3.1
LazyData: true
VignetteBuilder: knitr
URL: https://trigosteam.github.io/SPIAT/
Config/pak/sysreqs: libgdal-dev gdal-bin libgeos-dev libmagick++-dev
        gsfonts libicu-dev libssl-dev libproj-dev libsqlite3-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:18:57 UTC
RemoteUrl: https://github.com/bioc/SPIAT
RemoteRef: RELEASE_3_22
RemoteSha: 60e740ae4b0537639ed3ec5ca8a104fa83afa4ae
NeedsCompilation: no
Packaged: 2025-11-11 17:48:00 UTC; root
Author: Anna Trigos [aut] (ORCID: <https://orcid.org/0000-0002-5915-2952>),
  Yuzhou Feng [aut, cre] (ORCID: <https://orcid.org/0000-0002-2955-4053>),
  Tianpei Yang [aut],
  Mabel Li [aut],
  John Zhu [aut],
  Volkan Ozcoban [aut],
  Maria Doyle [aut]
Maintainer: Yuzhou Feng <yuzhou0610@gmail.com>
Built: R 4.5.2; ; 2025-11-11 17:53:53 UTC; windows
