Voyager

DOI: 10.18129/B9.bioc.Voyager    

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

From geospatial to spatial omics

Bioconductor version: Development (3.17)

Voyager to SpatialFeatureExperiment (SFE) is just like scater to SingleCellExperiment. While SFE is a new S4 class, Voyager implements basic exploratory spatial data analysis (ESDA) methods for SFE. This first version supports univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Voyager also implements plotting functions to plot SFE data and ESDA results. Multivariate ESDA and univariate local metrics will be added in later versions.

Author: Lambda Moses [aut, cre] , Lior Pachter [aut, ths]

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")

# 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")

 

HTML	R Script	Functionality overview
PDF		Reference Manual

Details

biocViews	GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version	1.1.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	BiocParallel, bluster, ggnewscale, ggplot2, Matrix, methods, patchwork, rlang, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, SpatialFeatureExperiment, spdep, stats, SummarizedExperiment
LinkingTo
Suggests	BiocSingular, BiocStyle, cowplot, ExperimentHub, hexbin, knitr, rmarkdown, scater, scattermore, scran, SFEData, sparseMatrixStats, testthat (>= 3.0.0), vdiffr
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_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/Voyager/
Package Downloads Report	Download Stats