{
  "_id": "6a1052d8acfb0bcc41ca18f0",
  "Package": "SpatialExperimentIO",
  "Title": "Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as\nSpatialExperiment object",
  "Version": "1.5.0",
  "Authors@R": "c(\nperson(\"Yixing E.\", \"Dong\",\nemail = \"estelladong729@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0003-5115-5686\")))",
  "URL": "https://github.com/estellad/SpatialExperimentIO",
  "BugReports": "https://github.com/estellad/SpatialExperimentIO/issues",
  "Description": "Read in imaging-based spatial transcriptomics technology\ndata. Current available modules are for Xenium by 10X Genomics,\nCosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from\nBroad Institute. You can choose to read the data in as a\nSpatialExperiment or a SingleCellExperiment object.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "DataRepresentation, DataImport, Infrastructure,\nTranscriptomics, SingleCell, Spatial, GeneExpression",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:18 UTC",
  "RemoteUrl": "https://github.com/bioc/SpatialExperimentIO",
  "RemoteRef": "HEAD",
  "RemoteSha": "56f593fd6df67215b6250df3298befb8528d4245",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-09 09:10:15 UTC",
    "User": "root"
  },
  "Author": "Yixing E. Dong [aut, cre] (ORCID:\n<https://orcid.org/0009-0003-5115-5686>)",
  "Maintainer": "Yixing E. Dong <estelladong729@gmail.com>",
  "MD5sum": "7ed6752f37e2b935e009c6d2f01ad017",
  "_user": "bioc",
  "_type": "src",
  "_file": "SpatialExperimentIO_1.5.0.tar.gz",
  "_fileid": "1062b3ea533e8520fca310c87f527dbd491390a0ba433781eda5830252eb821d",
  "_filesize": 532231,
  "_sha256": "1062b3ea533e8520fca310c87f527dbd491390a0ba433781eda5830252eb821d",
  "_created": "2026-05-09T09:10:15.000Z",
  "_published": "2026-05-22T12:58:00.584Z",
  "_jobs": [
    {
      "job": 77383863076,
      "time": 201,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6894570458"
    },
    {
      "job": 77383862866,
      "time": 375,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6894585951"
    },
    {
      "job": 77383862591,
      "time": 374,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6894586276"
    },
    {
      "job": 77383863038,
      "time": 215,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6894588010"
    },
    {
      "job": 77383862731,
      "time": 285,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6894590481"
    },
    {
      "job": 77383862176,
      "time": 297,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6894552601"
    },
    {
      "job": 77383862120,
      "time": 171,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7161034077"
    },
    {
      "job": 77383862642,
      "time": 258,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6894575567"
    },
    {
      "job": 77383862568,
      "time": 275,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6894577073"
    },
    {
      "job": 77383862525,
      "time": 300,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6894579451"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SpatialExperimentIO",
  "_commit": {
    "id": "56f593fd6df67215b6250df3298befb8528d4245",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381458
  },
  "_maintainer": {
    "name": "Yixing E. Dong",
    "email": "estelladong729@gmail.com",
    "login": "estellad",
    "uuid": 29610938
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "DropletUtils",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "arrow",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "datarepresentation",
    "dataimport",
    "infrastructure",
    "transcriptomics",
    "singlecell",
    "spatial",
    "geneexpression"
  ],
  "_stars": 19,
  "_contributors": [
    {
      "user": "estellad",
      "count": 46,
      "uuid": 29610938
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 260,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SpatialExperimentIO"
  },
  "_devurl": "https://github.com/estellad/spatialexperimentio",
  "_searchresults": 63,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SpatialExperimentIO.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/estellad/spatialexperimentio",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addParquetPathsCosmx",
    "addParquetPathsXenium",
    "addParquetPathToMeta",
    "csvToParquetPaths",
    "readCosmxSXE",
    "readMerscopeSXE",
    "readSeqfishSXE",
    "readStarmapplusSXE",
    "readXeniumSXE"
  ],
  "_help": [
    {
      "page": "dot-sanityCheck",
      "title": "Sanity check if one and only file with the specified name pattern exists in the data download directory, and return the file path to .csv Used for count matrix and metadata only, as they require unique.",
      "topics": [
        ".sanityCheck"
      ]
    },
    {
      "page": "addParquetPathsCosMx",
      "title": "Add CosMx-related parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.",
      "topics": [
        "addParquetPathsCosmx"
      ]
    },
    {
      "page": "addParquetPathsXenium",
      "title": "Add Xenium-related parquet paths to metadata for transcripts or cell/nucleus boundaries.",
      "topics": [
        "addParquetPathsXenium"
      ]
    },
    {
      "page": "addParquetPathToMeta",
      "title": "Add parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.",
      "topics": [
        "addParquetPathToMeta"
      ]
    },
    {
      "page": "csvToParquetPaths",
      "title": "If transcripts or polygon is expected to be loaded, write a parquet file to the current data download (if not already), and return the file path to .parquet",
      "topics": [
        "csvToParquetPaths"
      ]
    },
    {
      "page": "readCosmxSXE",
      "title": "Load data from a Nanostring CosMx experiment",
      "topics": [
        "readCosmxSXE"
      ]
    },
    {
      "page": "readMerscopeSXE",
      "title": "Load data from a Vizgen MERSCOPE experiment",
      "topics": [
        "readMerscopeSXE"
      ]
    },
    {
      "page": "readSeqfishSXE",
      "title": "Load data from a Spatial Genomics seqFISH experiment",
      "topics": [
        "readSeqfishSXE"
      ]
    },
    {
      "page": "readStarmapplusSXE",
      "title": "Load data from a STARmap PLUS experiment",
      "topics": [
        "readStarmapplusSXE"
      ]
    },
    {
      "page": "readXeniumSXE",
      "title": "Load data from a 10x Geonomics Xenium experiment",
      "topics": [
        "readXeniumSXE"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SpatialExperimentIO/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "arrow",
    "askpass",
    "assertthat",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "dir.expiry",
    "dplyr",
    "dqrng",
    "DropletUtils",
    "edgeR",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "h5mread",
    "HDF5Array",
    "httr2",
    "IRanges",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pillar",
    "pkgconfig",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "Rcpp",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SpatialExperiment",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "SpatialExperimentIO.Rmd",
      "filename": "SpatialExperimentIO.html",
      "title": "SpatialExperimentIO - Data Reader Package Overview",
      "author": "Yixing E. Dong",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Quick Start",
        "Xenium",
        "Read Xenium as a SpatialExperiment object",
        "Read Xenium as a SingleCellExperiment object",
        "CosMx",
        "Read CosMx as a SpatialExperiment object",
        "Read CosMx as a SingleCellExperiment object",
        "MERSCOPE",
        "Read MERSCOPE as a SpatialExperiment object",
        "Read MERSCOPE as a SingleCellExperiment object",
        "STARmap PLUS",
        "Read STARmap PLUS as a SpatialExperiment object",
        "Read STARmap PLUS as a SingleCellExperiment object",
        "seqFISH",
        "Read seqFISH as a SpatialExperiment object",
        "Read seqFISH as a SingleCellExperiment object",
        "Session Info"
      ],
      "created": "2023-11-20 08:51:58",
      "modified": "2025-02-03 12:15:07",
      "commits": 9
    }
  ],
  "_score": 6.555215405126074,
  "_indexed": true,
  "_nocasepkg": "spatialexperimentio",
  "_universes": [
    "bioc",
    "estellad"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-05-09T09:14:31.000Z",
      "distro": "noble",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "7abb2c908608a6ea1487193401faf1f846684bc437b844782c17e6a351329857",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-05-09T09:14:39.000Z",
      "distro": "noble",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "bd5a4249667b7b9830c8ebbf937d2f9a4c5e4c895f9759d3de88ce7e71a40141",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-05-09T09:15:36.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "bd1551ff49bda50769c3aea3ef4c6dbd6a0287057e9b608bdff214f558db8116",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-05-09T09:15:14.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "a4519a1cb171bf4423e253cb725485aaaf2a0c456df828f2b197e009af45fed3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-09T09:12:23.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "f43fa27b5a7a96aa87884b2ca3ce6e3d106d8a4322f7990b2ad4be0844314c9b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-09T09:12:21.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "520563a80733206e70dbe917d81119a61d6f3d1e7b2a9a6849fbe4213d21d314",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-05-09T09:13:11.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "05b8ae480252d9fa1761a291175746a9a486392ef61609e1c4d1637d8538ed37",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.0",
      "date": "2026-05-22T12:57:33.000Z",
      "commit": "56f593fd6df67215b6250df3298befb8528d4245",
      "fileid": "a54261126b7c46aae7f1f3caba35a1fdbc813cebef9c35f7341446614f52e934",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25597254430"
    }
  ]
}