Package: Voyager
Type: Package
Title: From geospatial to spatial omics
Version: 1.10.0
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'
git_url: https://git.bioconductor.org/packages/Voyager
git_branch: RELEASE_3_21
git_last_commit: 27b5859
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 04:24:16 UTC; biocbuild
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 4.5.0; ; 2025-04-16 15:48:00 UTC; windows
