Package: SpatialFeatureExperiment
Type: Package
Title: Integrating SpatialExperiment with Simple Features in sf
Version: 1.15.0
Authors@R: 
    c(person("Lambda", "Moses", email = "dl3764@columbia.edu", 
    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 = "lpachter@caltech.edu",
    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' 'rotateMinRect.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, OSTA.data, 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 (>= 4.3.0)
VignetteBuilder: knitr
biocViews: DataRepresentation, Transcriptomics, Spatial
URL: https://pachterlab.github.io/SpatialFeatureExperiment
BugReports: https://github.com/pachterlab/SpatialFeatureExperiment/issues
Config/pak/sysreqs: libabsl-dev cmake libfftw3-dev libgdal-dev gdal-bin
        libgeos-dev make libmagick++-dev gsfonts libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libuv1-dev libssl-dev libproj-dev
        libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:59:09 UTC
RemoteUrl: https://github.com/bioc/SpatialFeatureExperiment
RemoteRef: HEAD
RemoteSha: df605bf0b08c1b5511b9f5cdb8ccfc8307402350
NeedsCompilation: no
Packaged: 2026-05-29 10:09:17 UTC; root
Author: Lambda Moses [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7092-9427>),
  Alik Huseynov [aut] (ORCID: <https://orcid.org/0000-0002-1438-4389>),
  Lior Pachter [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-9164-6231>)
Maintainer: Lambda Moses <dl3764@columbia.edu>