Voyager
This is the development version of Voyager; for the stable release version, see Voyager.
From geospatial to spatial omics
Bioconductor version: Development (3.24)
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] 
, Alik Huseynov [aut] , Kayla Jackson [aut] , Laura Luebbert [aut] , Lior Pachter [aut, rev]
Maintainer: Lambda Moses <lambda.calc29 at gmail.com>
citation("Voyager")):Lambda Moses, Alik Huseynov, Kayla Jackson, Laura Luebbert, Lior Pachter. Voyager: From geospatial to spatial omics. doi:10.18129/B9.bioc.Voyager, R package version 1.15.2, https://bioconductor.org/packages/Voyager.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.15.2 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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 |
See More
| Suggests | arrow, automap, BiocSingular, BiocStyle, biscale, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scrapper, sfarrow, SFEData, spatialreg, testthat (>= 3.0.0), vdiffr, xml2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | alabaster.sfe, SpatialFeatureExperiment |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Voyager_1.15.2.tar.gz |
| Windows Binary (x86_64) | Voyager_1.15.2.zip |
| macOS Binary (big-sur-x86_64) | Voyager_1.15.2.tgz |
| macOS Binary (sonoma-arm64) | Voyager_1.15.2.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 |