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Voyager

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

From geospatial to spatial omics


Bioconductor version: Development (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] , Kayla Jackson [aut] , Laura Luebbert [aut] , Lior Pachter [aut, rev]

Maintainer: Lambda Moses <dlu2 at caltech.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Voyager")

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("Voyager")
Functionality overview HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/pachterlab/voyager
Bug Reports https://github.com/pachterlab/voyager/issues
See More
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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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Voyager_1.5.0.tar.gz
Windows Binary Voyager_1.5.0.zip
macOS Binary (x86_64) Voyager_1.5.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Voyager
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Voyager
Bioc Package Browser https://code.bioconductor.org/browse/Voyager/
Package Short Url https://bioconductor.org/packages/Voyager/
Package Downloads Report Download Stats