{
  "_id": "6a1fcfebb401979e73433d6c",
  "Package": "SpatialArtifacts",
  "Title": "Identification and Classification of Spatial Artifacts in Visium\nand Visium HD Data",
  "Version": "1.1.0",
  "Authors@R": "c(person(\"Harriet Jiali\", \"He\", email = \"jhe46@jh.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0003-7827-2735\")),\nperson(\"Jacqueline R.\", \"Thompson\", email = \"jthom338@jh.edu\", role = \"aut\"),\nperson(\"Michael\", \"Totty\", email = \"mtotty2@jh.edu\", role = \"aut\"),\nperson(\"Stephanie C.\", \"Hicks\", email = \"shicks19@jhu.edu\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0002-7858-0231\")))",
  "Description": "SpatialArtifacts provides a data-driven two-step workflow\nto identify, classify, and handle spatial artifacts in spatial\ntranscriptomics data. The package combines median absolute\ndeviation (MAD)-based outlier detection with morphological\nimage processing (fill, outline, and star patterns) to detect\nedge and interior artifacts. It supports multiple platforms\nincluding 10x Genomics Visium (standard and HD), allowing for\nconsistent quality control across different spatial\nresolutions.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/CambridgeCat13/SpatialArtifacts",
  "BugReports": "https://github.com/CambridgeCat13/SpatialArtifacts/issues",
  "biocViews": "Software, Spatial, Transcriptomics, QualityControl,\nDataImport, WorkflowStep, Classification",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "SystemRequirements": "quarto, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>=\n4.8.0)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libmagick++-dev\ngsfonts libicu-dev libssl-dev libproj-dev libsqlite3-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-04 19:58:20 UTC",
  "RemoteUrl": "https://github.com/bioc/SpatialArtifacts",
  "RemoteRef": "HEAD",
  "RemoteSha": "699127a618c09d2e66f5e3f9b07697e0367adc81",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 06:47:02 UTC",
    "User": "root"
  },
  "Author": "Harriet Jiali He [aut, cre] (ORCID:\n<https://orcid.org/0009-0003-7827-2735>),\nJacqueline R. Thompson [aut],\nMichael Totty [aut],\nStephanie C. Hicks [aut, fnd] (ORCID:\n<https://orcid.org/0000-0002-7858-0231>)",
  "Maintainer": "Harriet Jiali He <jhe46@jh.edu>",
  "MD5sum": "992b110d0efb46029b27779a1cfc4e89",
  "_user": "bioc",
  "_type": "src",
  "_file": "SpatialArtifacts_1.1.0.tar.gz",
  "_fileid": "4670094a23eaad97955500eed3dc50152a4764fd9943cd4d63abc6094f7b62bf",
  "_filesize": 7740357,
  "_sha256": "4670094a23eaad97955500eed3dc50152a4764fd9943cd4d63abc6094f7b62bf",
  "_created": "2026-06-03T06:47:02.000Z",
  "_published": "2026-06-03T06:55:39.580Z",
  "_jobs": [
    {
      "job": 79237638700,
      "time": 167,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7377623859"
    },
    {
      "job": 79237638706,
      "time": 443,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7377700341"
    },
    {
      "job": 79237638737,
      "time": 426,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7377695674"
    },
    {
      "job": 79237638847,
      "time": 277,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7377654665"
    },
    {
      "job": 79237638724,
      "time": 345,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7377673198"
    },
    {
      "job": 79236928103,
      "time": 307,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7377577289"
    },
    {
      "job": 79237638749,
      "time": 167,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7377623567"
    },
    {
      "job": 79237638715,
      "time": 301,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7377661810"
    },
    {
      "job": 79237638736,
      "time": 367,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7377679530"
    },
    {
      "job": 79237638692,
      "time": 371,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7377680583"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SpatialArtifacts",
  "_commit": {
    "id": "699127a618c09d2e66f5e3f9b07697e0367adc81",
    "author": "Jiali He <jialihe@umich.edu>",
    "committer": "Jiali He <jialihe@umich.edu>",
    "message": "bump version to 1.1.0, add gene symbols to rowData of spe_vignette\n",
    "time": 1777924700
  },
  "_maintainer": {
    "name": "Harriet Jiali He",
    "email": "jhe46@jh.edu",
    "login": "cambridgecat13",
    "description": "",
    "uuid": 166168135
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "scuttle",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "terra",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocCheck",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 14
    },
    {
      "week": "2026-10",
      "n": 7
    },
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-13",
      "n": 4
    },
    {
      "week": "2026-14",
      "n": 7
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "spatial",
    "transcriptomics",
    "qualitycontrol",
    "dataimport",
    "workflowstep",
    "classification"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "cambridgecat13",
      "count": 32,
      "uuid": 166168135
    },
    {
      "user": "stephaniehicks",
      "count": 6,
      "uuid": 1452065
    },
    {
      "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": 132,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SpatialArtifacts"
  },
  "_devurl": "https://github.com/cambridgecat13/spatialartifacts",
  "_searchresults": 9,
  "_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/SpatialArtifacts.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cambridgecat13/spatialartifacts",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "classifyEdgeArtifacts",
    "clumpEdges",
    "detectEdgeArtifacts",
    "detectEdgeArtifacts_Visium",
    "detectEdgeArtifacts_VisiumHD",
    "focal_transformations",
    "focal_transformations_terra",
    "problemAreas",
    "problemAreas_WithMorphology_terra"
  ],
  "_datasets": [
    {
      "name": "spe_vignette",
      "title": "Example SpatialExperiment for Vignettes",
      "object": "spe_vignette",
      "class": [
        "SpatialExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SpatialArtifacts-package",
      "title": "SpatialArtifacts: Detect and Classify Spatial Artifacts",
      "topics": [
        "SpatialArtifacts-package",
        "SpatialArtifacts"
      ]
    },
    {
      "page": "classifyEdgeArtifacts",
      "title": "Classify Edge Artifacts into Hierarchical Categories",
      "topics": [
        "classifyEdgeArtifacts"
      ]
    },
    {
      "page": "clumpEdges",
      "title": "Detect edge dryspots using spatial clustering",
      "topics": [
        "clumpEdges"
      ]
    },
    {
      "page": "detectEdgeArtifacts",
      "title": "Unified Edge Artifact Detection",
      "topics": [
        "detectEdgeArtifacts"
      ]
    },
    {
      "page": "detectEdgeArtifacts_Visium",
      "title": "Detect edge artifacts in spatial transcriptomics data",
      "topics": [
        "detectEdgeArtifacts_Visium"
      ]
    },
    {
      "page": "detectEdgeArtifacts_VisiumHD",
      "title": "Detect Edge Artifacts in VisiumHD Data",
      "topics": [
        "detectEdgeArtifacts_VisiumHD"
      ]
    },
    {
      "page": "focal_transformations",
      "title": "Apply morphological transformations to identify connected outlier regions",
      "topics": [
        "focal_transformations"
      ]
    },
    {
      "page": "focal_transformations_terra",
      "title": "Morphological transformations using terra (optimized for VisiumHD)",
      "topics": [
        "focal_transformations_terra"
      ]
    },
    {
      "page": "problemAreas",
      "title": "Identify all problem areas in spatial transcriptomics data",
      "topics": [
        "problemAreas"
      ]
    },
    {
      "page": "problemAreas_WithMorphology_terra",
      "title": "Detect problem areas in VisiumHD data using morphological processing",
      "topics": [
        "problemAreas_WithMorphology_terra"
      ]
    },
    {
      "page": "spe_vignette",
      "title": "Example SpatialExperiment for Vignettes",
      "topics": [
        "spe_vignette"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/SpatialArtifacts/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/SpatialArtifacts/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr2",
    "IRanges",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "terra",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "hippocampus-edge-detection.Rmd",
      "filename": "hippocampus-edge-detection.html",
      "title": "SpatialArtifacts Tutorial",
      "author": "Harriet Jiali He, Stephanie C. Hicks",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Input data format",
        "Platform Support",
        "Two key steps",
        "The detection phase",
        "The classification phase",
        "Helpful information on parameters",
        "Platform selection",
        "Example use cases",
        "Parameters for detectEdgeArtifacts()",
        "For all platforms",
        "For standard Visium",
        "For VisiumHD",
        "Parameters for classifyEdgeArtifacts()",
        "Platform Comparison Summary",
        "Understanding the output columns",
        "Example: Standard Visium workflow",
        "Data preparation: converting to dense matrix",
        "VisiumHD Workflow Example",
        "VisiumHD 16µm Resolution Example",
        "VisiumHD 8µm Resolution Example",
        "Key VisiumHD Considerations",
        "Visualization: QC Metrics and Detection Results",
        "Classification Summary",
        "Final Classification Summary",
        "Raw Edge Detection Summary",
        "Quality Control Validation",
        "Filtering Out Problematic Spots (Optional)",
        "Conclusion",
        "Session Information"
      ],
      "created": "2026-02-26 05:09:42",
      "modified": "2026-04-03 16:11:34",
      "commits": 7
    }
  ],
  "_score": 5.505149978319906,
  "_indexed": true,
  "_nocasepkg": "spatialartifacts",
  "_universes": [
    "bioc",
    "cambridgecat13"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-03T06:50:40.000Z",
      "distro": "noble",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "eea07ce6b0d449e8e1e6eb58420aa6e83f49032d91e7390818840723ede0a4a9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-06-03T06:50:39.000Z",
      "distro": "noble",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "4156b68d9fbf57ac94a87886e84a82c12f245a6778f022b7a5a0d8f50ec36913",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-03T06:49:21.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "825e17319035b9886ab69fcfd0ecd39b9e4a2846b760237bb998f99612ea091b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-06-03T06:49:27.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "8546562ed3241b94ad0abfe7a23948e8fdf03f9c6cc528ec54a5673d2969bb4c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-06-03T06:50:25.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "c3f2d05581ade8708961dbc6ae66794765362bb790150453559d480c463b08ef",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-03T06:49:29.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "3171ae024bb65721cf050880cb7072588a81ffc83923955abf31b395e0b43761",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-03T06:49:00.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "9779d3759f0245b28f68b8d98bff01c79a1038b8c6d10167134818c87825a81a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-06-03T06:49:02.000Z",
      "commit": "699127a618c09d2e66f5e3f9b07697e0367adc81",
      "fileid": "1cb9f2c98c314c890282c614ea5cdce8c9c93a7dc69482c099488462cb0e1f7a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26868268790"
    }
  ]
}