{ "_id": "6ad09eef576abc75bd5cdc10", "Package": "XeniumIO", "Type": "Package", "Title": "Import and represent Xenium data from the 10X Xenium Analyzer", "Version": "1.5.0", "Authors@R": "c(\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\", c(\"aut\", \"cre\"),\nc(ORCID = \"0000-0002-3242-0582\")\n),\nperson(\"Dario\", \"Righelli\", role = \"ctb\"),\nperson(\"Estella\", \"Dong\", role = \"ctb\"),\nperson(\"NCI\", role = \"fnd\", comment = c(GrantNo. = \"U24CA289073\"))\n)", "Description": "The package allows users to readily import spatial data\nobtained from the 10X Xenium Analyzer pipeline. Supported\nformats include 'parquet', 'h5', and 'mtx' files. The package\nmainly represents data as SpatialExperiment objects.", "License": "Artistic-2.0", "biocViews": "Software, Infrastructure, DataImport, SingleCell, Spatial", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "BugReports": "https://github.com/waldronlab/XeniumIO/issues", "URL": "https://github.com/waldronlab/XeniumIO", "Collate": "'XeniumFile.R' 'TENxXenium-class.R' 'XeniumIO-package.R'\n'utilities.R'", "Date": "2025-12-11", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibmagick++-dev gsfonts libicu-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev libx11-dev zlib1g-dev", "Repository": "https://waldronlab.r-universe.dev", "Date/Publication": "2026-04-28 13:04:26 UTC", "RemoteUrl": "https://github.com/waldronlab/XeniumIO", "RemoteRef": "HEAD", "RemoteSha": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 09:25:02 UTC", "User": "root" }, "Author": "Marcel Ramos [aut, cre] (ORCID:\n),\nDario Righelli [ctb],\nEstella Dong [ctb],\nNCI [fnd] (GrantNo.: U24CA289073)", "Maintainer": "Marcel Ramos ", "_user": "waldronlab", "_type": "src", "_file": "XeniumIO_1.5.0.tar.gz", "_fileid": "https://r2.ropensci.org/de25781ef630e9a84400c028edc75ffddd541155ac5d8a9885899d68bc5af09c", "_filesize": 121663, "_sha256": "de25781ef630e9a84400c028edc75ffddd541155ac5d8a9885899d68bc5af09c", "_expires": "2027-01-23T09:37:10.000Z", "_created": "2026-10-15T09:25:02.000Z", "_published": "2026-10-15T09:37:51.582Z", "_buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116348290826, "time": 260, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11961736186" }, { "job": 116348290987, "time": 259, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11960939641" }, { "job": 116348290708, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11962055156" }, { "job": 116348291216, "time": 221, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11961324958" }, { "job": 116346379246, "time": 273, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11961277836" }, { "job": 116348290822, "time": 136, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11961263338" }, { "job": 116348290914, "time": 210, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11960904206" }, { "job": 116348290816, "time": 211, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11961780545" }, { "job": 116348290841, "time": 202, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11961672483" } ], "_upstream": "https://github.com/waldronlab/XeniumIO", "_commit": { "id": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381466 }, "_maintainer": { "name": "Marcel Ramos", "email": "marcel.ramos@sph.cuny.edu", "login": "link-ny", "bluesky": "@mramos148.bsky.social", "linkedin": "in/mramos148", "orcid": "0000-0002-3242-0582", "twitter": "@M2RuseR", "description": "Sr. Data Scientist @ CUNY School of Public Health: Waldron Lab & Bioconductor Core Team Member / \nR 📦 dev ", "uuid": 4392950 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "TENxIO", "role": "Depends" }, { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "BiocBaseUtils", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "BiocIO", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "VisiumIO", "version": ">= 1.7.5", "role": "Imports" }, { "package": "arrow", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" } ], "_owner": "waldronlab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-50", "n": 7 }, { "week": "2026-13", "n": 3 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "infrastructure", "dataimport", "singlecell", "spatial", "u24ca289073" ], "_stars": 0, "_contributors": [ { "user": "link-ny", "count": 48, "uuid": 4392950 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "copilot", "count": 1, "uuid": 198982749 } ], "_userbio": { "uuid": 15236403, "type": "organization", "name": "Waldron Lab at the CUNY SPH", "followers": 119, "description": "Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/XeniumIO" }, "_devurl": "https://github.com/waldronlab/xeniumio", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/XeniumIO.html" ], "_homeurl": "https://github.com/waldronlab/xeniumio", "_realowner": "bioc", "_cranurl": true, "_exports": [ "import", "TENxXenium", "XeniumFile" ], "_help": [ { "page": "XeniumIO-package", "title": "XeniumIO: Import and represent Xenium data from the 10X Xenium Analyzer", "topics": [ "XeniumIO-package", "XeniumIO" ] }, { "page": "TENxXenium-class", "title": "A class to represent Xenium output data", "topics": [ ".TENxXenium", "import,TENxXenium,ANY,ANY-method", "TENxXenium", "TENxXenium-class" ] }, { "page": "XeniumFile-class", "title": "A minimal class to represent Xenium metadata", "topics": [ ".XeniumFile", "import,XeniumFile,ANY,ANY-method", "XeniumFile", "XeniumFile-class" ] } ], "_readme": "https://github.com/waldronlab/XeniumIO/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "bit", "bit64", "blob", "cachem", "class", "classInt", "cli", "clipr", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dir.expiry", "dplyr", "e1071", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "h5mread", "HDF5Array", "hms", "httr2", "IRanges", "jsonlite", "KernSmooth", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "prettyunits", "progress", "proxy", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "Rcpp", "readr", "rhdf5", "rhdf5filters", "Rhdf5lib", "rjson", "rlang", "RSQLite", "s2", "S4Arrays", "S4Vectors", "Seqinfo", "sf", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "TENxIO", "tibble", "tidyr", "tidyselect", "tzdb", "units", "utf8", "vctrs", "VisiumIO", "vroom", "withr", "wk", "XVector" ], "_vignettes": [ { "source": "XeniumIO.Rmd", "filename": "XeniumIO.html", "title": "XeniumIO: Import 10X Genomics Xenium Analyzer Data", "author": "Marcel Ramos", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Supported Formats", "TENxIO", "VisiumIO", "XeniumIO", "Installation", "Loading package", "Example Folder Structure", "Xenium class", "import method", "Importing an Example Xenium Dataset", "Session Info" ], "created": "2024-10-01 21:09:50", "modified": "2025-12-11 22:04:38", "commits": 13 } ], "_score": 4.6020599913279625, "_indexed": false, "_nocasepkg": "xeniumio", "_universes": [ "waldronlab" ], "_indexurl": "https://bioc.r-universe.dev/XeniumIO", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-10-15T09:27:43.000Z", "distro": "resolute", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/58970556c3e64ad4199c5ed3c59bb3ea43be22a1b3fc24267bb45614e37c246a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0", "date": "2026-10-15T09:27:43.000Z", "distro": "resolute", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/568f093b5513a337cfabaf0089bedec9d219330e459a6cfe2115ebc17fa40f46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-10-15T09:30:52.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/46e5b2349e9ffe45f097233365fdf200bfb94e1ce194ded19fb7100d3b4c1d8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0", "date": "2026-10-15T09:34:21.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/54dd8525c9c23e7b9d0aaff4cdf0d70928882b98f6b1aac48903ac19b8f97039", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-10-15T09:27:51.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/702a69f51d5c1e1db44e5cbfc2cc664817f3f443decf7cc0fdab42808eb6753b", "status": "success", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-10-15T09:26:38.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/60e7adde0e6f6a883e6fed9fa15b19cd4e430d32965e695868e924f0cff66cbb", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-10-15T09:26:48.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/5ffc71205e9f5de4e94582902b202982d596fe272b847ab757984d9d25438f8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" }, { "r": "4.6.1", "os": "win", "version": "1.5.0", "date": "2026-10-15T09:26:36.000Z", "commit": "0e7d3811a3460c4fb05672b41fd0ed64d62d1b71", "fileid": "https://r2.ropensci.org/9ec377089a98daa1dbbcccaf44ce4eaf5805549dea264fb967733f148a533628", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/38712250405" } ] }