{ "_id": "6a19386bacfb0bcc41dd35e8", "Package": "visiumStitched", "Title": "Enable downstream analysis of Visium capture areas stitched\ntogether with Fiji", "Version": "1.5.0", "Date": "2025-10-22", "Authors@R": "c(\nperson(\"Nicholas J.\", \"Eagles\", email = \"nickeagles77@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9808-5254\")),\nperson(\"Leonardo\", \"Collado-Torres\", role = c(\"ctb\"),\nemail = \"lcolladotor@gmail.com\", comment = c(ORCID = \"0000-0003-2140-308X\"))\n)", "Description": "This package provides helper functions for working with\nmultiple Visium capture areas that overlap each other. This\npackage was developed along with the companion example use case\ndata available from\nhttps://github.com/LieberInstitute/visiumStitched_brain.\nvisiumStitched prepares SpaceRanger (10x Genomics) output files\nso you can stitch the images from groups of capture areas\ntogether with Fiji. Then visiumStitched builds a\nSpatialExperiment object with the stitched data and makes an\nartificial hexagonal grid enabling the seamless use of spatial\nclustering methods that rely on such grid to identify\nneighboring spots, such as PRECAST and BayesSpace. The\nSpatialExperiment objects created by visiumStitched are\ncompatible with spatialLIBD, which can be used to build\ninteractive websites for stitched SpatialExperiment objects.\nvisiumStitched also enables casting SpatialExperiment objects\nas Seurat objects.", "License": "Artistic-2.0", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "biocViews": "Software, Spatial, Transcriptomics, Transcription,\nGeneExpression, Visualization, DataImport", "URL": "https://github.com/LieberInstitute/visiumStitched", "BugReports": "https://support.bioconductor.org/tag/visiumStitched", "Config/pak/sysreqs": "libcairo2-dev cmake libfftw3-dev libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libmagick++-dev gsfonts libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev\nlibwebp-dev libxml2-dev libssl-dev perl libx11-dev xz-utils\nzlib1g-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": { "Date": "2026-05-29 06:24:27 UTC", "User": "root" }, "Author": "Nicholas J. Eagles [aut, cre] (ORCID:\n),\nLeonardo Collado-Torres [ctb] (ORCID:\n)", "Maintainer": "Nicholas J. Eagles ", "MD5sum": "b0752b9a373a2a7163608252804b43cd", "_user": "bioc", "_type": "src", "_file": "visiumStitched_1.5.0.tar.gz", "_fileid": "42f7ee77e7ad0502a42fda3f948ef507be6efac4f49c8773dc0939efe685716a", "_filesize": 2589101, "_sha256": "42f7ee77e7ad0502a42fda3f948ef507be6efac4f49c8773dc0939efe685716a", "_created": "2026-05-29T06:24:27.000Z", "_published": "2026-05-29T06:55:39.785Z", "_jobs": [ { "job": 78449367205, "time": 293, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7284525933" }, { "job": 78449367321, "time": 840, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284656727" }, { "job": 78449367227, "time": 835, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7284655577" }, { "job": 78449367228, "time": 520, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7284873991" }, { "job": 78449367236, "time": 542, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7284875532" }, { "job": 78448190887, "time": 617, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284458418" }, { "job": 78449367199, "time": 225, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7284509902" }, { "job": 78449367267, "time": 1447, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7284797739" }, { "job": 78449367252, "time": 1317, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7284768275" }, { "job": 78449367257, "time": 1625, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7284838789" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26621455978", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/visiumStitched", "_commit": { "id": "4a0e0e4531b5755bd686086f340f3836aeadfc6e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381443 }, "_maintainer": { "name": "Nicholas J. 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