{
  "_id": "6a4990a16d67900babdfbce8",
  "Package": "Seqtometry",
  "Title": "Signature scoring for single cell analysis",
  "Version": "1.1.0",
  "URL": "https://github.com/HawigerLab/Seqtometry",
  "BugReports": "https://github.com/HawigerLab/Seqtometry/issues",
  "Authors@R": "c( \nperson(\"Robert\", \"Kousnetsov\", email = \"robert.kousnetsov@health.slu.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Daniel\", \"Hawiger\", email = \"daniel.hawiger@health.slu.edu\", role = c(\"cph\", \"fnd\")))",
  "Description": "This package provides functions used in Seqtometry\n(Kousnetsov et al. 2024), a method for analyzing single cell\n(scRNA-seq or scATAC-seq) data via signature (gene set)\nenrichment scores. The Seqtometry scores may be useful for\nannotating or characterizing cells, either in a flow cytometry\nlike workflow (where scores are standalone features used for\nprogressive partitoning as described in the Seqtometry\npublication) or in a cluster-based workflow (as features of\nclusters). The exported impute function (a port of Python's\nMAGIC-impute, van Dijk et al. 2018), may also be useful for\nsingle cell analysis on its own.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "SingleCell, GeneSetEnrichment, GeneExpression",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:37 UTC",
  "RemoteUrl": "https://github.com/bioc/Seqtometry",
  "RemoteRef": "HEAD",
  "RemoteSha": "a787eb929f0d3ef2329f325eb97bc352363b114d",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 22:37:15 UTC",
    "User": "root"
  },
  "Author": "Robert Kousnetsov [aut, cre],\nDaniel Hawiger [cph, fnd]",
  "Maintainer": "Robert Kousnetsov <robert.kousnetsov@health.slu.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "Seqtometry_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e29304c1ea212c3331793086e81779e58d7da4fddc76ad7cb98894a99b7d25f0",
  "_filesize": 826598,
  "_sha256": "e29304c1ea212c3331793086e81779e58d7da4fddc76ad7cb98894a99b7d25f0",
  "_expires": "2026-10-12T23:00:47.000Z",
  "_created": "2026-07-04T22:37:15.000Z",
  "_published": "2026-07-04T23:00:49.078Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 3
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875",
  "_status": "success",
  "_upstream": "https://github.com/bioc/Seqtometry",
  "_commit": {
    "id": "a787eb929f0d3ef2329f325eb97bc352363b114d",
    "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": 1777381597
  },
  "_maintainer": {
    "name": "Robert Kousnetsov",
    "email": "robert.kousnetsov@health.slu.edu",
    "login": "hawigerlab",
    "description": "",
    "uuid": 153688213
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85172763329,
      "time": 227,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086075208"
    },
    {
      "job": 85172763341,
      "time": 378,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086092013"
    },
    {
      "job": 85172763345,
      "time": 511,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086106158"
    },
    {
      "job": 85172763343,
      "time": 379,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086092101"
    },
    {
      "job": 85172763400,
      "time": 491,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086103906"
    },
    {
      "job": 85172763382,
      "time": 300,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086083525"
    },
    {
      "job": 85172763394,
      "time": 479,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086102728"
    },
    {
      "job": 85172763423,
      "time": 301,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086083559"
    },
    {
      "job": 85172763346,
      "time": 584,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086113922"
    },
    {
      "job": 85172413444,
      "time": 358,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086049479"
    },
    {
      "job": 85172763323,
      "time": 228,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8086075235"
    },
    {
      "job": 85172763391,
      "time": 1321,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8086193273"
    },
    {
      "job": 85172763406,
      "time": 1355,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8086196591"
    },
    {
      "job": 85172763393,
      "time": 1283,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8086189516"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RcppHNSW",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "zeallot",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "box",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "harmony",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "scuttle",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "sparseMatrixStats",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "TENxPBMCData",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-02",
      "n": 3
    },
    {
      "week": "2026-03",
      "n": 1
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "singlecell",
    "genesetenrichment",
    "geneexpression",
    "cpp"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "hawigerlab",
      "count": 8,
      "uuid": 153688213
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/hawigerlab/seqtometry",
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_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/Seqtometry.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hawigerlab/seqtometry",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "impute",
    "score"
  ],
  "_help": [
    {
      "page": "Seqtometry-package",
      "title": "Signature scoring for single cell analysis",
      "topics": [
        "Seqtometry-package",
        "Seqtometry"
      ]
    },
    {
      "page": "dot-apply_diff_op",
      "title": "Perform data diffusion",
      "topics": [
        ".apply_diff_op"
      ]
    },
    {
      "page": "dot-calc_diff_op",
      "title": "Compute diffusion operator",
      "topics": [
        ".calc_diff_op"
      ]
    },
    {
      "page": "dot-calc_pca",
      "title": "PCA wrapper",
      "topics": [
        ".calc_pca"
      ]
    },
    {
      "page": "dot-check_params",
      "title": "Parameter validation",
      "topics": [
        ".check_params"
      ]
    },
    {
      "page": "dot-gene_indices",
      "title": "Finds row indices of signature genes",
      "topics": [
        ".gene_indices"
      ]
    },
    {
      "page": "dot-invert_pca",
      "title": "PCA inversion",
      "topics": [
        ".invert_pca"
      ]
    },
    {
      "page": "dot-minmax_scale",
      "title": "Minmax transform",
      "topics": [
        ".minmax_scale"
      ]
    },
    {
      "page": "dot-normalize",
      "title": "LogCP10K transform",
      "topics": [
        ".normalize"
      ]
    },
    {
      "page": "dot-procrustes",
      "title": "Procrustes disparity",
      "topics": [
        ".procrustes"
      ]
    },
    {
      "page": "impute",
      "title": "MAGIC imputation (van Dijk et al. 2018)",
      "topics": [
        "impute"
      ]
    },
    {
      "page": "score",
      "title": "Seqtometry scoring (Kousnetsov et al. 2024)",
      "topics": [
        "score"
      ]
    },
    {
      "page": "wks",
      "title": "Helper function for performing a weighted Kolmogorov-Smirnov-like procedure.",
      "topics": [
        "wks"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Seqtometry/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "backports",
    "beachmat",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "BiocSingular",
    "checkmate",
    "cli",
    "codetools",
    "cpp11",
    "data.table",
    "DelayedArray",
    "digest",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "globals",
    "glue",
    "IRanges",
    "irlba",
    "lambda.r",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "parallelly",
    "purrr",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "rlang",
    "RSpectra",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "snow",
    "SparseArray",
    "vctrs",
    "XVector",
    "zeallot"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Seqtometry.Rmd",
      "filename": "Seqtometry.html",
      "title": "Seqtometry vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Basic workflow",
        "Retrieve data and signatures",
        "Preprocessing and imputation",
        "Score and plot data"
      ],
      "created": "2026-01-11 19:27:09",
      "modified": "2026-03-15 00:59:34",
      "commits": 2
    }
  ],
  "_score": 4.544068044350276,
  "_indexed": true,
  "_nocasepkg": "seqtometry",
  "_universes": [
    "bioc",
    "hawigerlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-04T22:41:05.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/97d50e5890b7f60d39981e953e83b8972fe2698d26e530d953caeb594d8b082f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-04T22:42:15.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/09cb39a85244b44b72a76ac53c929507874e15fb8a4e8aad297d78a4573ea944",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-04T22:41:12.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/e3cc280ba319bb83edb1e003551f13355c175794784c2287e926007f9c852dda",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-04T22:42:30.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/e23e7ec98195bb474f29e4b870725be60725e4fa75c1540984bc851b00ff9f32",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T22:39:38.000Z",
      "arch": "aarch64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/fe878c88629ca89289ac52dd78b01520e76f1bc372941deb86a7ae56c8682f2c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T22:41:06.000Z",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/276d16249793499def36ad31f74ae53305e033e05fb9b07c50835caabe394bd5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T22:39:35.000Z",
      "arch": "aarch64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/bd0924eb5fc3f403a4fa497e0e66615bab2eaf5317d07dc0ebd50ed9561ef231",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T22:41:10.000Z",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/73b3dda5412edda8a4156869ec875cb14d624a078cdd131393aff8d27a763fa8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-07-04T22:41:26.000Z",
      "arch": "emscripten",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/dfdc365513b4e8eee36549a821d47d7174e316ff23468bcd4df9dece166c89a3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-04T22:55:10.000Z",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/308f4fb5f8b455f7c455a5ff66d0493e37757ea9a3994f3aada34b4a2f171422",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-04T22:54:53.000Z",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/c162a55b9a83cefd6f4b564332d17e9ef25b9b6ccb958430b5b4f868da774f88",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-04T22:54:23.000Z",
      "arch": "x86_64",
      "commit": "a787eb929f0d3ef2329f325eb97bc352363b114d",
      "fileid": "https://r2.ropensci.org/d663279897c2948556d449989614da9b0dc9883017c720efe92ee3c332a3c97b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721747875"
    }
  ]
}