Voyager
This is thereleased version of Voyager; for the devel version, seeVoyager.
From geospatial to spatial omics
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0002-7092-9427, Alik Huseynov [aut] ORCID: 0000-0002-1438-4389, Kayla Jackson [aut] ORCID: 0000-0001-6483-0108, Laura Luebbert [aut] ORCID: 0000-0003-1379-2927, Lior Pachter [aut, rev] ORCID: 0000-0002-9164-6231
Maintainer: Lambda Moses <dl3764 at columbia.edu>
citation("Voyager")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("Voyager")For older versions of R, please refer to the appropriateBioconductor 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 | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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,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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | alabaster.sfe,SpatialFeatureExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | Voyager_1.12.0.tar.gz |
| Windows Binary (x86_64) | Voyager_1.12.0.zip |
| macOS Binary (x86_64) | Voyager_1.12.0.tgz |
| macOS Binary (arm64) | Voyager_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Voyager |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Voyager |
| Bioc Package Browser | https://code.bioconductor.org/browse/Voyager/ |
| Package Short Url | https://bioconductor.org/packages/Voyager/ |
| Package Downloads Report | Download Stats |