Package: Voyager
Type: Package
Title: From geospatial to spatial omics
Version: 1.12.0
Authors@R: 
    c(person("Lambda", "Moses", email = "dl3764@columbia.edu", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7092-9427")),
    person("Alik", "Huseynov",
    comment = c(ORCID = "0000-0002-1438-4389"),
    role = "aut"),
    person("Kayla", "Jackson", email = "kaylajac@caltech.edu",
    role = c("aut"),
    comment = c(ORCID = "0000-0001-6483-0108")),
    person("Laura", "Luebbert", email = "lauraluebbert@caltech.edu",
    role = c("aut"),
    comment = c(ORCID = "0000-0003-1379-2927")),
    person("Lior", "Pachter", email = "lpachter@caltech.edu",
    role = c("aut", "rev"),
    comment = c(ORCID = "0000-0002-9164-6231")))
Description: 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.
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, 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
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/testthat/edition: 3
biocViews: GeneExpression, Spatial, Transcriptomics, Visualization
VignetteBuilder: knitr
URL: https://github.com/pachterlab/voyager
BugReports: https://github.com/pachterlab/voyager/issues
Collate: 'AllGenerics.R' 'res2df.R' 'SFEMethod-class.R'
        'SFEMethod-bivariate.R' 'SFEMethod-multivariate.R'
        'SFEMethod-spdep.R' 'bivariate.R' 'data.R' 'featureData.R'
        'geom_spi.R' 'gstat.R' 'listSFEMethods.R' 'multivariate.R'
        'plot-non-spatial.R' 'plot-transcripts.R'
        'plot-univar-downstream.R' 'plot.R' 'plotLocalResult.R'
        'plotSpatialReducedDim.R' 'spatial-misc.R'
        'univariate-downstream.R' 'univariate-internal.R'
        'univariate.R' 'utils.R'
Config/pak/sysreqs: libabsl-dev cmake libfftw3-dev libgdal-dev gdal-bin
        libgeos-dev libglpk-dev make libmagick++-dev gsfonts libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libxml2-dev libssl-dev
        libproj-dev libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:19:14 UTC
RemoteUrl: https://github.com/bioc/Voyager
RemoteRef: RELEASE_3_22
RemoteSha: d689ab87e12f2ea69d39e3352058afec727aa702
NeedsCompilation: no
Packaged: 2025-11-11 18:23:57 UTC; root
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>)
Maintainer: Lambda Moses <dl3764@columbia.edu>
Built: R 4.5.2; ; 2025-11-12 03:15:33 UTC; windows
