Package: SpatialFeatureExperiment
Type: Package
Title: Integrating SpatialExperiment with Simple Features in sf
Version: 1.11.1
Authors@R: 
    c(person("Lambda", "Moses", email = "[email protected]", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7092-9427")),
    person("Alik", "Huseynov",
    comment = c(ORCID = "0000-0002-1438-4389"),
    role = "aut"),
    person("Lior", "Pachter", email = "[email protected]",
    role = c("aut", "ths"),
    comment = c(ORCID = "0000-0002-9164-6231")))
Description: A new S4 class integrating Simple Features with the R package sf
    to bring geospatial data analysis methods based on vector data to
    spatial transcriptomics. Also implements management of spatial neighborhood
    graphs and geometric operations. This pakage builds upon SpatialExperiment
    and SingleCellExperiment, hence methods for these parent classes can still
    be used.
Imports:
    Biobase,
    BiocGenerics (>= 0.51.2),
    BiocNeighbors,
    BiocParallel,
    data.table,
    DropletUtils,
    EBImage,
    grDevices,
    lifecycle,
    Matrix,
    methods,
    rjson,
    rlang,
    S4Vectors,
    sf,
    sfheaders,
    SingleCellExperiment,
    SpatialExperiment,
    spatialreg,
    spdep (>= 1.1-7),
    SummarizedExperiment,
    stats,
    terra,
    utils,
    zeallot
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.3
Collate: 
    'AllGenerics.R'
    'utils.R'
    'SFE-class.R'
    'aggregate.R'
    'align.R'
    'annotGeometries.R'
    'cbind.R'
    'changeSampleIDs.R'
    'coerce.R'
    'data.R'
    'debris.R'
    'df2sf.R'
    'dimGeometries.R'
    'featureData.R'
    'formatTxSpots.R'
    'geometry_operation.R'
    'graph_wrappers.R'
    'image.R'
    'int_dimData.R'
    'internal-Voyager.R'
    'listw2sparse.R'
    'localResults.R'
    'read.R'
    'reexports.R'
    'saveRDS.R'
    'spatialGraphs.R'
    'split.R'
    'subset.R'
    'tissue_boundary.R'
    'transformation.R'
    'updateObject.R'
    'validity.R'
    'zzz.R'
Suggests: 
    arrow,
    BiocStyle,
    dplyr,
    gmp,
    knitr,
    RBioFormats,
    rhdf5,
    rmarkdown,
    scater,
    sfarrow,
    SFEData (>= 1.5.3),
    Seurat,
    SeuratObject,
    sparseMatrixStats,
    testthat (>= 3.0.0),
    tidyr,
    VisiumIO,
    Voyager (>= 1.7.2),
    withr,
    xml2
Remotes:
    Voyager=github::pachterlab/voyager@devel
Config/testthat/edition: 3
Depends: 
    R (>= 4.2.0)
VignetteBuilder: knitr
biocViews:
    DataRepresentation,
    Transcriptomics,
    Spatial
URL: https://github.com/pachterlab/SpatialFeatureExperiment
BugReports: https://github.com/pachterlab/SpatialFeatureExperiment/issues