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DESCRIPTION
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DESCRIPTION
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Package: SpatialFeatureExperiment
Type: Package
Title: Integrating SpatialExperiment with Simple Features in sf
Version: 1.6.1
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,
BiocNeighbors,
BiocParallel,
data.table,
DropletUtils,
EBImage,
grDevices,
lifecycle,
Matrix,
methods,
rjson,
rlang,
S4Vectors,
sf,
sfheaders,
SingleCellExperiment,
SpatialExperiment,
spdep (>= 1.1-7),
SummarizedExperiment,
stats,
terra,
utils,
zeallot
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Collate:
'AllGenerics.R'
'utils.R'
'SFE-class.R'
'annotGeometries.R'
'cbind.R'
'coerce.R'
'data.R'
'df2sf.R'
'dimGeometries.R'
'featureData.R'
'formatTxSpots.R'
'geometry_operation.R'
'graph_wrappers.R'
'image.R'
'int_dimData.R'
'internal-Voyager.R'
'localResults.R'
'read.R'
'reexports.R'
'saveRDS.R'
'spatialGraphs.R'
'subset.R'
'transformation.R'
'updateObject.R'
'validity.R'
Suggests:
arrow,
BiocStyle,
knitr,
RBioFormats,
rhdf5,
rmarkdown,
sfarrow,
SFEData (>= 1.5.3),
testthat (>= 3.0.0),
Voyager,
xml2,
scater,
Seurat,
SeuratObject,
dplyr,
tidyr
Remotes:
Voyager=github::pachterlab/voyager
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