Voyager

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 caltech.edu>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Functionality overview
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom
SystemRequirements
Enhances
URL	https://github.com/pachterlab/voyager
BugReports	https://github.com/pachterlab/voyager/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Voyager_1.2.7.tar.gz
Windows Binary	Voyager_1.2.7.zip
macOS Binary (x86_64)	Voyager_1.2.7.tgz
macOS Binary (arm64)	Voyager_1.2.7.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
Old Source Packages for BioC 3.17	Source Archive