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SpatialFeatureExperiment

Integrating SpatialExperiment with Simple Features in sf

Bioconductor version: Release (3.17)

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] , 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 "4.3") and enter: 

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

BiocManager::install("SpatialFeatureExperiment")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpatialFeatureExperiment")
Introduction to the SpatialFeatureExperiment class HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, Software, Spatial, Transcriptomics
Version 1.2.2
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports BiocGenerics, BiocNeighbors, BiocParallel, grDevices, Matrix, methods, rjson, rlang, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils
Linking To
Suggests BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/pachterlab/SpatialFeatureExperiment
Bug Reports https://github.com/pachterlab/SpatialFeatureExperiment/issues
See More
Depends On Me
Imports Me Voyager
Suggests Me SFEData
Links To Me
Build Report  

Package Archives

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

Source Package SpatialFeatureExperiment_1.2.2.tar.gz
Windows Binary SpatialFeatureExperiment_1.2.2.zip
macOS Binary (x86_64) SpatialFeatureExperiment_1.2.2.tgz
macOS Binary (arm64) SpatialFeatureExperiment_1.2.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpatialFeatureExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialFeatureExperiment
Bioc Package Browser https://code.bioconductor.org/browse/SpatialFeatureExperiment/
Package Short Url https://bioconductor.org/packages/SpatialFeatureExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive