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From geospatial to spatial omics

Bioconductor version: Release (3.19)

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] , Alik Huseynov [aut] , Kayla Jackson [aut] , Laura Luebbert [aut] , Lior Pachter [aut, rev]

Maintainer: Lambda Moses <dlu2 at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Functionality overview HTML R Script
Reference Manual PDF


biocViews GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), SpatialFeatureExperiment(>= 1.5.2)
Imports BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils
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Suggests automap, BiocSingular, BiocStyle, cowplot, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom, xml2
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Follow Installation instructions to use this package in your R session.

Source Package Voyager_1.6.0.tar.gz
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macOS Binary (x86_64) Voyager_1.6.0.tgz
macOS Binary (arm64) Voyager_1.6.0.tgz
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