DOI: 10.18129/B9.bioc.Voyager  

From geospatial to spatial omics

Bioconductor version: Release (3.17)

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

Author: Lambda Moses [aut, cre] , Kayla Jackson [aut] , Laura Luebbert [aut] , Lior Pachter [aut, rev]

Maintainer: Lambda Moses <dlu2 at>

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biocViews GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version 1.2.7
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, SpatialFeatureExperiment(>= 1.2.1), spdep, stats, SummarizedExperiment, terra, utils
Suggests automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom
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