SpatialFeatureExperiment

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Integrating SpatialExperiment with Simple Features in sf

Bioconductor version: Development (3.24)

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: 0000-0002-7092-9427 , Alik Huseynov [aut] ORCID: 0000-0002-1438-4389 , Lior Pachter [aut, ths] ORCID: 0000-0002-9164-6231

Maintainer: Lambda Moses <lambda.calc29 at gmail.com>

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

Lambda Moses, Alik Huseynov, Lior Pachter. SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf. doi:10.18129/B9.bioc.SpatialFeatureExperiment, R package version 1.15.0, https://bioconductor.org/packages/SpatialFeatureExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Software, Spatial, Transcriptomics
Version	1.15.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	Artistic-2.0
Depends	R (>= 4.3.0)
Imports	Biobase, BiocGenerics (>= 0.51.2), BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot
System Requirements
URL	https://pachterlab.github.io/SpatialFeatureExperiment
Bug Reports	https://github.com/pachterlab/SpatialFeatureExperiment/issues

Suggests	arrow, BiocStyle, dplyr, duckspatial, gmp, knitr, OSTA.data, RBioFormats, rhdf5, rmarkdown, scrapper, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, VisiumIO, Voyager (>= 1.7.2), withr, xml2
Linking To
Enhances
Depends On Me	alabaster.sfe, Voyager
Imports Me	TENxXeniumData
Suggests Me	concordexR, imageFeatureTCGA, imageTCGAutils, jazzPanda, MultiAssaySpatialExperiment, multipointR, SFEData, xenLite
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SpatialFeatureExperiment_1.15.0.tar.gz
Windows Binary (x86_64)	SpatialFeatureExperiment_1.15.0.zip
macOS Binary (big-sur-x86_64)	SpatialFeatureExperiment_1.15.0.tgz
macOS Binary (sonoma-arm64)	SpatialFeatureExperiment_1.15.0.tgz
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/
Package Downloads Report	Download Stats