“Everything is related to everything else. But near things are more related than distant things.” - Tobler’s first law of geography
This package brings the tradition of geospatial statistics to spatial omics by wrapping classical geospatial packages such as
gstat to be used with the
SpatialFeatureExperiment class, which extends SpatialExperiment with sf. This is the
Voyager R documentation website. Documentation for the Python implementation is available here. Questions, suggestions, or problems should be submitted as GitHub issues.
SpatialFeatureExperiment were developed within the Bioconductor ecosystem, and build on several existing objects and tools. Single cell RNA-seq data and metadata can be represented with
SingleCellExperiment S4 class objects, and these can be utilized for exploratory data analysis and visualization using the
scuttle packages. The
SpatialExperiment class extends
SingleCellExperiments to allow for representation of spatial genomics data.
SpatialExperiment with Simple Features from
SpatialFeatureExperiment is as
Voyager also builds on the geospatial tradition, especially the
spdep package, which is one of the main R packages for spatial dependence analyses. Specifically,
Voyager focuses on spatial autocorrelation, which measures the extent of similarity or dissimilarity of spatially proximal regions, and that can be quantified in terms of length scale, and variation in space.
Voyager can be installed from Bioconductor version 3.16 or higher:
Voyager: exploratory single-cell genomics data analysis with geospatial statistics Lambda Moses, Pétur Helgi Einarsson, Kayla Jackson, Laura Luebbert, A. Sina Booeshaghi, Sindri Antonsson, Páll Melsted, Lior Pachter bioRxiv 2023.07.20.549945; doi: https://doi.org/10.1101/2023.07.20.549945