Package: visiumStitched
Title: Enable downstream analysis of Visium capture areas stitched
        together with Fiji
Version: 1.5.0
Date: 2025-10-22
Authors@R: 
    c(
    person("Nicholas J.", "Eagles", email = "nickeagles77@gmail.com",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9808-5254")),
    person("Leonardo", "Collado-Torres", role = c("ctb"), 
    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X"))
    )
Description: This package provides helper functions for working with
        multiple Visium capture areas that overlap each other. This
        package was developed along with the companion example use case
        data available from
        https://github.com/LieberInstitute/visiumStitched_brain.
        visiumStitched prepares SpaceRanger (10x Genomics) output files
        so you can stitch the images from groups of capture areas
        together with Fiji. Then visiumStitched builds a
        SpatialExperiment object with the stitched data and makes an
        artificial hexagonal grid enabling the seamless use of spatial
        clustering methods that rely on such grid to identify
        neighboring spots, such as PRECAST and BayesSpace. The
        SpatialExperiment objects created by visiumStitched are
        compatible with spatialLIBD, which can be used to build
        interactive websites for stitched SpatialExperiment objects.
        visiumStitched also enables casting SpatialExperiment objects
        as Seurat objects.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4), SpatialExperiment
Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR,
        rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Imports: BiocBaseUtils, BiocGenerics, clue, dplyr, DropletUtils,
        grDevices, imager, Matrix, methods, pkgcond, readr, rjson,
        S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8),
        stringr, SummarizedExperiment, tibble, tidyr, xml2
biocViews: Software, Spatial, Transcriptomics, Transcription,
        GeneExpression, Visualization, DataImport
URL: https://github.com/LieberInstitute/visiumStitched
BugReports: https://support.bioconductor.org/tag/visiumStitched
Config/pak/sysreqs: cmake libfftw3-dev libglpk-dev make libmagick++-dev
        gsfonts libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libtiff-dev libuv1-dev libxml2-dev libssl-dev perl
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:04:03 UTC
RemoteUrl: https://github.com/bioc/visiumStitched
RemoteRef: HEAD
RemoteSha: 4a0e0e4531b5755bd686086f340f3836aeadfc6e
NeedsCompilation: no
Packaged: 2026-07-03 21:54:45 UTC; root
Author: Nicholas J. Eagles [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9808-5254>),
  Leonardo Collado-Torres [ctb] (ORCID:
    <https://orcid.org/0000-0003-2140-308X>)
Maintainer: Nicholas J. Eagles <nickeagles77@gmail.com>