Voyager
From geospatial to spatial omics
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Voyager")Details
| Maintainer | Lambda Moses <dl3764@columbia.edu> |
| Author | Lambda Moses [aut, cre] (ORCID: <https://orcid.org/0000-0002-7092-9427>), Alik Huseynov [aut] (ORCID: <https://orcid.org/0000-0002-1438-4389>), Kayla Jackson [aut] (ORCID: <https://orcid.org/0000-0001-6483-0108>), Laura Luebbert [aut] (ORCID: <https://orcid.org/0000-0003-1379-2927>), Lior Pachter [aut, rev] (ORCID: <https://orcid.org/0000-0002-9164-6231>) |
| License | Artistic-2.0 |
| URL | https://github.com/pachterlab/voyager |
| Bug Reports | https://github.com/pachterlab/voyager/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Software, Spatial, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/Voyager/ |
Citation
From within R, enter 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 1.14.0, https://bioconductor.org/packages/Voyager.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Voyager_1.14.0.tar.gz |
| Windows binary (x86_64) | Voyager_1.14.0.zip |
| macOS binary (arm64) | Voyager_1.14.0.tgz |
| macOS binary (x86_64) | Voyager_1.14.0.tgz |
Dependencies
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
Suggests: arrow, automap, BiocSingular, BiocStyle, biscale, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2
Reverse dependencies
Suggests Me (2): alabaster.sfe, SpatialFeatureExperiment