{
  "_id": "6ad1daa129625c14e47aebe1",
  "Package": "SpotSweeper",
  "Title": "Spatially-aware quality control for spatial transcriptomics",
  "Version": "1.9.3",
  "Date": "2026-10-15",
  "Authors@R": "c(\nperson(\"Michael\", \"Totty\", email = \"mictott@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9292-8556\")),\nperson(\"Stephanie\", \"Hicks\", email = \"shicks19@jhu.edu\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7858-0231\")),\nperson(\"Boyi\", \"Guo\", email = \"boyi.guo.work@gmail.com\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2950-2349\")))",
  "Description": "Spatially-aware quality control (QC) software for both\nspot-level and artifact-level QC in spot-based spatial\ntranscriptomics, such as 10x Visium. These methods calculate\nlocal (nearest-neighbors) mean and variance of standard QC\nmetrics (library size, unique genes, and mitochondrial\npercentage) to identify outlier spots and large technical\nartifacts.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/MicTott/SpotSweeper",
  "BugReports": "https://support.bioconductor.org/tag/SpotSweeper",
  "biocViews": "Software, Spatial, Transcriptomics, QualityControl,\nGeneExpression,",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "LazyData": "False",
  "News": "NEWS.md",
  "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-16 02:22:19 UTC",
  "RemoteUrl": "https://github.com/bioc/SpotSweeper",
  "RemoteRef": "HEAD",
  "RemoteSha": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-16 07:29:52 UTC",
    "User": "root"
  },
  "Author": "Michael Totty [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9292-8556>),\nStephanie Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>),\nBoyi Guo [aut] (ORCID: <https://orcid.org/0000-0003-2950-2349>)",
  "Maintainer": "Michael Totty <mictott@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "SpotSweeper_1.9.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/148c4530cbbd0d505481879e432a2d9e6e5cf437176e2563b7f071d74c3f1a8c",
  "_filesize": 3500950,
  "_sha256": "148c4530cbbd0d505481879e432a2d9e6e5cf437176e2563b7f071d74c3f1a8c",
  "_expires": "2027-01-24T08:04:47.000Z",
  "_created": "2026-10-16T07:29:52.000Z",
  "_published": "2026-10-16T08:04:49.326Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_upstream": "https://github.com/bioc/SpotSweeper",
  "_commit": {
    "id": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
    "author": "Michael Totty <mictott@gmail.com>",
    "committer": "Michael Totty <mictott@gmail.com>",
    "message": "Fix Windows parallel nearest-neighbor search\n\nSelect socket workers automatically on Windows in localOutliers and localVariance while preserving the workers interface. Add native and socket parallel regression coverage and bump to 1.9.3. Fixes #27.\n",
    "time": 1792117339
  },
  "_maintainer": {
    "name": "Michael Totty",
    "email": "mictott@gmail.com",
    "login": "mictott",
    "twitter": "@MicTott",
    "description": "",
    "uuid": 32395683,
    "orcid": "0000-0002-9292-8556"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 116864092782,
      "time": 207,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12031269039"
    },
    {
      "job": 116864092844,
      "time": 487,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12031819232"
    },
    {
      "job": 116864092769,
      "time": 467,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12032406298"
    },
    {
      "job": 116864093097,
      "time": 351,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12032513558"
    },
    {
      "job": 116864092831,
      "time": 406,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12033567078"
    },
    {
      "job": 116862173008,
      "time": 341,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12031607761"
    },
    {
      "job": 116864092780,
      "time": 186,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12032017295"
    },
    {
      "job": 116864092897,
      "time": 485,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12032087944"
    },
    {
      "job": 116864092778,
      "time": 489,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12031404667"
    },
    {
      "job": 116864092911,
      "time": 384,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12032127405"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocNeighbors",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "escheR",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scuttle",
      "role": "Suggests"
    },
    {
      "package": "STexampleData",
      "role": "Suggests"
    },
    {
      "package": "ggpubr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-43",
      "n": 2
    },
    {
      "week": "2026-37",
      "n": 3
    },
    {
      "week": "2026-42",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "spatial",
    "transcriptomics",
    "qualitycontrol",
    "geneexpression",
    "bioconductor",
    "quality-control",
    "spatial-transcriptomics"
  ],
  "_stars": 17,
  "_contributors": [
    {
      "user": "mictott",
      "count": 189,
      "uuid": 32395683
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "boyiguo1",
      "count": 4,
      "uuid": 16565218
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 561,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SpotSweeper"
  },
  "_devurl": "https://github.com/mictott/spotsweeper",
  "_searchresults": 198,
  "_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/SpotSweeper.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/mictott/spotsweeper",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "findArtifacts",
    "flagVisiumOutliers",
    "getMetadata",
    "getSpatialCoords",
    "localOutliers",
    "localVariance",
    "plotQCmetrics",
    "plotQCpdf",
    "setMetadata",
    "subsetSpatialObject",
    "validateMetadataColumns"
  ],
  "_datasets": [
    {
      "name": "biased_spots",
      "title": "Biased Spots Data",
      "object": "biased_spots",
      "file": "biased_spots.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "row",
        "col",
        "barcode"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    },
    {
      "name": "DLPFC_artifact",
      "title": "human DLPFC dataset with a technical artifact (hangnail).",
      "object": "DLPFC_artifact",
      "file": "DLPFC_artifact.rda",
      "class": [
        "SpatialExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "biased_spots",
      "title": "Biased Spots Data",
      "topics": [
        "biased_spots"
      ]
    },
    {
      "page": "DLPFC_artifact",
      "title": "human DLPFC dataset with a technical artifact (hangnail).",
      "topics": [
        "DLPFC_artifact"
      ]
    },
    {
      "page": "findArtifacts",
      "title": "Identify and annotate artifacts in spatial transcriptomics data",
      "topics": [
        "findArtifacts"
      ]
    },
    {
      "page": "flagVisiumOutliers",
      "title": "Flag systematic Visium outlier positions",
      "topics": [
        "flagVisiumOutliers"
      ]
    },
    {
      "page": "getMetadata",
      "title": "Get column metadata from a spatial object",
      "topics": [
        "getMetadata"
      ]
    },
    {
      "page": "getSpatialCoords",
      "title": "Get spatial coordinates from a spatial object",
      "topics": [
        "getSpatialCoords"
      ]
    },
    {
      "page": "localOutliers",
      "title": "Detect local outliers in spatial transcriptomics data",
      "topics": [
        "localOutliers"
      ]
    },
    {
      "page": "localVariance",
      "title": "localVariance Function",
      "topics": [
        "localVariance"
      ]
    },
    {
      "page": "plotQCmetrics",
      "title": "Plot QC metrics for a Single Sample in a SpatialExperiment object",
      "topics": [
        "plotQCmetrics"
      ]
    },
    {
      "page": "plotQCpdf",
      "title": "Plot Outlier Metrics to PDF",
      "topics": [
        "plotQCpdf"
      ]
    },
    {
      "page": "setMetadata",
      "title": "Replace column metadata in a spatial object",
      "topics": [
        "setMetadata"
      ]
    },
    {
      "page": "subsetSpatialObject",
      "title": "Subset a spatial object by spots",
      "topics": [
        "subsetSpatialObject"
      ]
    },
    {
      "page": "validateMetadataColumns",
      "title": "Validate columns in spatial-object metadata",
      "topics": [
        "validateMetadataColumns"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SpotSweeper/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "escheR",
    "farver",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "httr2",
    "IRanges",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "getting_started.Rmd",
      "filename": "getting_started.html",
      "title": "Getting started with 'SpotSweeper'",
      "author": "Michael Totty, Boyi Guo, Stephanie Hicks",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Assay and chemistry support",
        "Installation",
        "Spot-level local outlier detection",
        "Loading example data",
        "Calculating QC metrics using scuttle",
        "Identifying local outliers using SpotSweeper",
        "Using a Seurat object",
        "Visualizing local outliers",
        "Removing technical artifacts using SpotSweeper",
        "Visualizing technical artifacts",
        "Identifying artifacts using SpotSweeper",
        "Visualizing artifacts",
        "Session information"
      ],
      "created": "2024-02-13 23:11:26",
      "modified": "2026-09-08 21:48:21",
      "commits": 15
    }
  ],
  "_score": 7.657447880134812,
  "_indexed": true,
  "_nocasepkg": "spotsweeper",
  "_universes": [
    "bioc",
    "mictott"
  ],
  "_previous": "1.9.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-10-16T07:34:33.000Z",
      "distro": "resolute",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/b5041822a87a0d33e946818558949df6a77506cb19023103f6985e28228c670a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.3",
      "date": "2026-10-16T07:34:45.000Z",
      "distro": "resolute",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/f0dce2b285c0c6d8b76a0e4d538d98d199281f65a450f514df5b8ff1b27978d6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-10-16T08:00:29.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/89bfcca4bb920d2b9e9d2a480f5fee5b94a30ec59611383cb313f2bc8994b6e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.3",
      "date": "2026-10-16T07:59:32.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/da9ec81335d585fab2041635ecb4429108b55082ef596af9ee74f7a65ce458a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.3",
      "date": "2026-10-16T07:33:34.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/7f87a30dd784998195c146562ed3b39fbc8f9b6e40a7de9ae019012e66fd39ea",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-10-16T07:34:10.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/13aba6942f961011a767a89e36d7a2edfdece7d8e271234764a82cc3e005bd9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-10-16T07:34:46.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/cd8cdad84361b95a351a71afbb33631cfe076146daa78bebaff79145cf27735c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.3",
      "date": "2026-10-16T07:34:00.000Z",
      "commit": "7e6ebf68c205cf0c102d8ed6b363752d5288d179",
      "fileid": "https://r2.ropensci.org/6ade375d85b8c3de61fabaa8439e91821b6780f7d171da10acec856081195421",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38867021529"
    }
  ]
}