{ "_id": "6a4a0d2db9bf02698bd56501", "Package": "SpotSweeper", "Title": "Spatially-aware quality control for spatial transcriptomics", "Version": "1.9.0", "Date": "2025-10-14", "Authors@R": "c(\nperson(\"Michael\", \"Totty\", ,\"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\ntranscripomics, 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 outliers spot 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": "7.3.1", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "LazyData": "False", "News": "NEWS.md", "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 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:01 UTC", "RemoteUrl": "https://github.com/bioc/SpotSweeper", "RemoteRef": "HEAD", "RemoteSha": "5c89af852985e2674b985f2f2f614639b15e6762", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-10 06:44:00 UTC", "User": "root" }, "Author": "Michael Totty [aut, cre] (ORCID:\n),\nStephanie Hicks [aut] (ORCID: ),\nBoyi Guo [aut] (ORCID: )", "Maintainer": "Michael Totty ", "_user": "bioc", "_type": "src", "_file": "SpotSweeper_1.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/efe58ab3638c619b6638adebc4fe67fc8c3d733188b1028fd6ca748a635eb898", "_filesize": 3472164, "_sha256": "efe58ab3638c619b6638adebc4fe67fc8c3d733188b1028fd6ca748a635eb898", "_expires": "2026-10-13T07:52:11.000Z", "_created": "2026-06-10T06:44:00.000Z", "_published": "2026-07-05T07:52:13.657Z", "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249", "_status": "success", "_upstream": "https://github.com/bioc/SpotSweeper", "_commit": { "id": "5c89af852985e2674b985f2f2f614639b15e6762", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381381 }, "_maintainer": { "name": "Michael Totty", "email": "mictott@gmail.com", "login": "mictott", "twitter": "@MicTott", "description": "", "uuid": 32395683, "orcid": "0000-0002-9292-8556" }, "_distro": "noble", "_jobs": [ { "job": 85204561070, "time": 289, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7528484579" }, { "job": 85204561062, "time": 550, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7528555943" }, { "job": 85204561154, "time": 541, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7528553120" }, { "job": 85204561066, "time": 398, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7528524738" }, { "job": 85204561133, "time": 441, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7528549551" }, { "job": 85204561053, "time": 384, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7528403260" }, { "job": 85204561151, "time": 229, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7528467842" }, { "job": 85204561128, "time": 615, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7528573890" }, { "job": 85204561129, "time": 580, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7528564164" }, { "job": 85204561103, "time": 548, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7528555290" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "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": "spatialEco", "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" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "software", "spatial", "transcriptomics", "qualitycontrol", "geneexpression", "bioconductor", "quality-control", "spatial-transcriptomics" ], "_stars": 16, "_contributors": [ { "user": "mictott", "count": 184, "uuid": 32395683 }, { "user": "boyiguo1", "count": 4, "uuid": 16565218 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 386, "source": "https://www.bioconductor.org/packages/stats/bioc/SpotSweeper" }, "_devurl": "https://github.com/mictott/spotsweeper", "_searchresults": 179, "_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/SpotSweeper.html", "manual.pdf" ], "_homeurl": "https://github.com/mictott/spotsweeper", "_realowner": "bioc", "_cranurl": false, "_exports": [ "findArtifacts", "flagVisiumOutliers", "localOutliers", "localVariance", "plotQCmetrics", "plotQCpdf" ], "_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 Visium Outliers in SpatialExperiment Objects", "topics": [ "flagVisiumOutliers" ] }, { "page": "localOutliers", "title": "localOutliers Function", "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" ] } ], "_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", "class", "classInt", "cli", "codetools", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "e1071", "escheR", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "httr2", "IRanges", "isoband", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "magick", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "proxy", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rjson", "rlang", "RSQLite", "s2", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "sf", "SingleCellExperiment", "snow", "SparseArray", "spatialEco", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "terra", "tibble", "tidyr", "tidyselect", "units", "utf8", "vctrs", "viridisLite", "withr", "wk", "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", "Installation", "Spot-level local outlier detection", "Loading example data", "Calculating QC metrics using scuttle", "Identifying local outliers using SpotSweeper", "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": "2024-11-08 19:37:17", "commits": 14 } ], "_score": 6.934094268355481, "_indexed": true, "_nocasepkg": "spotsweeper", "_universes": [ "bioc", "mictott" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-06-10T06:48:23.000Z", "distro": "noble", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/1543766484386e4b5dcc304b788e6066b67c07f0202563771d6478a86e34b609", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-06-10T06:48:24.000Z", "distro": "noble", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/1535656ad20e1d96ab6379513e2fe6e658514dd254b584273f85a281a68c6d64", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-06-10T06:47:24.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/b0aea5e3c7b2cb0b892c973db5a9447c4e95047bdcd80ef6064b9c3324c8df1b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-06-10T06:48:07.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/7199ad5aad738e4046db4ab58f9225a1686bfbfef64c1cb09b65bb1e21177c57", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-06-10T06:48:28.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/30f331377428e39bbffb3461de21bfc36883c3796b95340b9b190e179ffd0775", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:48:14.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/e0169f68f03f7c6fb83ecb26feba9c8a542b74c8226f6da81c3133ea82911524", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:48:24.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/b3f214b7cc3f5f4126939b48bb5b3010745d7b22ecf5a695f168371900d3ebd3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" }, { "r": "4.6.0", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:48:42.000Z", "commit": "5c89af852985e2674b985f2f2f614639b15e6762", "fileid": "https://r2.ropensci.org/d1077ff806421778d91fe20c10fcb495efe8193b4a34c9f24021600a1011a52c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258131249" } ] }