Package: visiumStitched
Title: Enable downstream analysis of Visium capture areas stitched
        together with Fiji
Version: 1.1.0
Date: 2024-11-21
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 hexogonal 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, 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
git_url: https://git.bioconductor.org/packages/visiumStitched
git_branch: devel
git_last_commit: 142b910
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:53:11 UTC; biocbuild
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 4.5.0; ; 2025-06-05 14:17:56 UTC; windows
