Voyager

DOI: 10.18129/B9.bioc.Voyager    

From geospatial to spatial omics

Bioconductor version: Release (3.16)

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. This first version supports univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. The Voyager package 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] , Kayla Jackson [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 "4.2") 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")

 

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PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Software, Spatial, Transcriptomics, Visualization
Version 1.0.4
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, dbscan, 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_1.0.4.tar.gz
Windows Binary Voyager_1.0.4.zip
macOS Binary (x86_64) Voyager_1.0.4.tgz
macOS Binary (arm64) Voyager_1.0.4.tgz
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
Old Source Packages for BioC 3.16 Source Archive

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