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 (3.21)

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] (ORCID: ), Alik Huseynov [aut] (ORCID: ), Lior Pachter [aut, ths] (ORCID: )

Maintainer: Lambda Moses <dl3764 at columbia.edu>

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

Installation

To install this package, start R (version "4.5") 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

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 1.9.0
In Bioconductor since BioC 3.16 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.2.0)
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
System Requirements
URL https://github.com/pachterlab/SpatialFeatureExperiment
Bug Reports https://github.com/pachterlab/SpatialFeatureExperiment/issues
See More
Suggests arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData(>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager(>= 1.7.2), xml2
Linking To
Enhances
Depends On Me
Imports Me TENxXeniumData
Suggests Me concordexR, xenLite, SFEData
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpatialFeatureExperiment_1.9.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser https://code.bioconductor.org/browse/SpatialFeatureExperiment/
Package Short Url https://bioconductor.org/packages/SpatialFeatureExperiment/
Package Downloads Report Download Stats