Package: visiumStitched
Title: Enable downstream analysis of Visium capture areas stitched
        together with Fiji
Version: 1.3.0
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: libcairo2-dev libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libwebp-dev
        libxml2-dev libssl-dev perl libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:33:12 UTC
RemoteUrl: https://github.com/bioc/visiumStitched
RemoteRef: HEAD
RemoteSha: 829e946d5c2b96e551ff1d0a9a5e1c72e6ecc6dd
NeedsCompilation: no
Packaged: 2025-10-30 15:33:06 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>
Built: R 4.6.0; ; 2025-10-30 15:37:48 UTC; windows
