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SpatialFeatureExperiment

This is the development version of SpatialFeatureExperiment; for the stable release version, see SpatialFeatureExperiment.

Integrating SpatialExperiment with Simple Features in sf


Bioconductor version: Development (3.19)

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.

Author: Lambda Moses [aut, cre] , Alik Huseynov [aut] , Lior Pachter [aut, ths]

Maintainer: Lambda Moses <dlu2 at caltech.edu>

Citation (from within R, enter citation("SpatialFeatureExperiment")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpatialFeatureExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews DataRepresentation, Software, Spatial, Transcriptomics
Version 1.5.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports 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
System Requirements GDAL (>= 3.8.0)
URL https://github.com/pachterlab/SpatialFeatureExperiment
Bug Reports https://github.com/pachterlab/SpatialFeatureExperiment/issues
See More
Suggests arrow, BiocStyle, knitr, RBioFormats, rhdf5, rmarkdown, SFEData(>= 1.5.3), testthat (>= 3.0.0), Voyager, xml2
Linking To
Enhances
Depends On Me
Imports Me TENxXeniumData, Voyager
Suggests Me SFEData
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SpatialFeatureExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialFeatureExperiment
Package Short Url https://bioconductor.org/packages/SpatialFeatureExperiment/
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