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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: