DESCRIPTION

Package: GiottoClass
Title: Giotto Suite object definitions and framework
Version: 0.4.5
Authors@R: c(
	person("Ruben", "Dries", email = "rubendries@gmail.com",
		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
	person("Jiaji", "George Chen", email = "jiajic@bu.edu",
		 role = c("aut")),
	person("Guo-Cheng", "Yuan", email = "guo-cheng.yuan@mssm.edu",
		 role = c("aut")),
    person("Matthew", "O'Brien", email = "mobrien2@bu.edu",
	     role = c("aut")),
	person("Joselyn C.", "Chávez-Fuentes", email = "joselynchavezf@gmail.com",
	     role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
	person("Edward", "Ruiz", email = "ecruiz@bu.edu",
		 role = c("aut"))
	)
Description: This package contains the Giotto object and subobject class
  definitions and frameworks. Functionalities relating to data ingestion, basic 
  object creation, data access within the Giotto object, and generics defined  
  for the Giotto classes are all found here. Applications of this framework and 
  convenience functions for loading specific technologies are found in the base 
  Giotto package.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
    R (>= 4.4.1)
Imports:
    checkmate,
    data.table (>= 1.12.2),
    dbscan (>= 1.1-3),
    deldir (>= 1.0.6),
    GiottoUtils (>= 0.2.0),
    graphics,
    grDevices,
    igraph (>= 1.2.4.1),
    magick,
    Matrix (>= 1.6-2),
    matrixStats (>= 0.55.0),
    methods,
    reticulate (>= 1.25),
    stats,
    terra (>= 1.7-41)
Suggests: 
    Biobase,
    chihaya,
    DelayedArray,
    DelayedMatrixStats (>= 1.24.0),
    exactextractr,
    geometry,
    GiottoData,
    HDF5Array (>= 1.18.1),
    knitr,
    plotly,
    raster,
    remotes,
    reshape2,
    rgl,
    rhdf5,
    rlang,
    rmarkdown,
    RTriangle (>= 1.6-0.10),
    S4Vectors,
    ScaledMatrix,
    scattermore,
    Seurat,
    SeuratObject,
    sf,
    SingleCellExperiment,
    sp,
    SpatialExperiment,
    stars,
    STexampleData,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    qs,
    xml2
Remotes: drieslab/GiottoUtils
Config/testthat/edition: 3
Collate: 
    'package_imports.R'
    'classes.R'
    'generics.R'
    'NN_network.R'
    'aggregate.R'
    'auxilliary.R'
    'buffer.R'
    'combine_metadata.R'
    'slot_accessors.R'
    'create.R'
    'data_evaluation.R'
    'data_input.R'
    'dd.R'
    'defaults.R'
    'flex_functions.R'
    'function_logging.R'
    'generate_poly.R'
    'giotto_structures.R'
    'globals.R'
    'gstop.R'
    'images.R'
    'instructions.R'
    'interoperability.R'
    'join.R'
    'methods-IDs.R'
    'methods-XY.R'
    'methods-affine.R'
    'methods-area.R'
    'methods-centroids.R'
    'methods-coerce.R'
    'methods-convHull.R'
    'methods-copy.R'
    'methods-crop.R'
    'methods-dims.R'
    'methods-ext.R'
    'methods-extract.R'
    'methods-flip.R'
    'methods-initialize.R'
    'methods-instructions.R'
    'methods-names.R'
    'methods-nesting.R'
    'methods-overlaps.R'
    'methods-plot.R'
    'methods-rbind.R'
    'methods-reconnect.R'
    'methods-relate.R'
    'methods-rescale.R'
    'methods-setGiotto.R'
    'methods-shear.R'
    'methods-show.R'
    'methods-spatShift.R'
    'methods-spin.R'
    'methods-transpose.R'
    'methods-wrap.R'
    'methods-zoom.R'
    'provenance.R'
    'python_bento.R'
    'python_environment.R'
    'save_load.R'
    'slot_check.R'
    'slot_list.R'
    'slot_show.R'
    'spatial_binary_ops.R'
    'spatial_query.R'
    'spatial_structures.R'
    'split.R'
    'stitch_coordinates.R'
    'subset.R'
    'suite_reexports.R'
    'zzz.R'
URL: https://drieslab.github.io/GiottoClass/
biocViews: Software, Technology, Spatial
VignetteBuilder: knitr
BugReports: https://github.com/drieslab/Giotto/issues