SpatialFeatureExperiment

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	Introduction to the SpatialFeatureExperiment class
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Software, Spatial, Transcriptomics
Version	1.2.3
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
LinkingTo
Suggests	BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/pachterlab/SpatialFeatureExperiment
BugReports	https://github.com/pachterlab/SpatialFeatureExperiment/issues
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_1.2.3.tar.gz
Windows Binary	SpatialFeatureExperiment_1.2.3.zip
macOS Binary (x86_64)	SpatialFeatureExperiment_1.2.3.tgz
macOS Binary (arm64)	SpatialFeatureExperiment_1.2.3.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