SpatialFeatureExperiment

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

Integrating SpatialExperiment with Simple Features in sf

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DOI: 10.18129/B9.bioc.SpatialFeatureExperiment

Bioconductor version: Development (3.23)

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

Maintainer: Lambda Moses <dl3764 at columbia.edu>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Software, Spatial, Transcriptomics

Version 1.13.0

In Bioconductor since BioC 3.16 (R-4.2) (3 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://github.com/pachterlab/SpatialFeatureExperiment

Bug Reports https://github.com/pachterlab/SpatialFeatureExperiment/issues

Suggests arrow, BiocStyle, dplyr, gmp, knitr, RBioFormats, rhdf5, rmarkdown, scater, 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, jazzPanda, 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_1.13.0.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/

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