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Bioconductor - SpatialFeatureExperiment (development version)

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 (3.22)

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 <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 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 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), 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.

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