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This is the development version of Voyager; for the stable release version, see Voyager.
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")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Voyager")
HTML | R Script | Functionality overview |
Reference Manual |
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 |
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 |
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