Voyager

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

From geospatial to spatial omics

Bioconductor version: Development (3.21)

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] (ORCID: ), Alik Huseynov [aut] (ORCID: ), Kayla Jackson [aut] (ORCID: ), Laura Luebbert [aut] (ORCID: ), Lior Pachter [aut, rev] (ORCID: )

Maintainer: Lambda Moses <dl3764 at columbia.edu>

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

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("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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version	1.9.2
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	Artistic-2.0
Depends	R (>= 4.2.0), SpatialFeatureExperiment(>= 1.7.3)
Imports	BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot
System Requirements
URL	https://github.com/pachterlab/voyager
Bug Reports	https://github.com/pachterlab/voyager/issues

Suggests	arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	SpatialFeatureExperiment
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	Voyager_1.9.2.tar.gz
Windows Binary (x86_64)	Voyager_1.9.2.zip
macOS Binary (x86_64)
macOS Binary (arm64)	Voyager_1.9.2.tgz
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