{
  "_id": "6a1ed86eb401979e7340f0df",
  "Package": "scooter",
  "Title": "Streamlined scRNA-Seq Analysis Pipeline",
  "Version": "0.0.0.9004",
  "Authors@R": "c(\nperson(\"Igor\", \"Dolgalev\", email = \"igor.dolgalev@nyumc.org\", role = c(\"cre\", \"aut\")),\nperson(\"Anna\", \"Yeaton\", email = \"ahyeaton@gmail.com\", role = \"aut\"))",
  "Description": "Streamlined scRNA-Seq analysis pipeline.",
  "License": "MIT + file LICENCE",
  "Encoding": "UTF-8",
  "biocViews": "",
  "RoxygenNote": "7.2.1",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 libx11-dev zlib1g-dev",
  "Repository": "https://igordot.r-universe.dev",
  "Date/Publication": "2023-11-17 22:09:58 UTC",
  "RemoteUrl": "https://github.com/igordot/scooter",
  "RemoteRef": "HEAD",
  "RemoteSha": "2a639459d3848e111717624497797441cfbf1747",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-20 09:48:51 UTC",
    "User": "root"
  },
  "Author": "Igor Dolgalev [cre, aut],\nAnna Yeaton [aut]",
  "Maintainer": "Igor Dolgalev <igor.dolgalev@nyumc.org>",
  "MD5sum": "9cf0c33216ee60c254f367e30885014b",
  "_user": "igordot",
  "_type": "src",
  "_file": "scooter_0.0.0.9004.tar.gz",
  "_fileid": "f5861e3700516f00e1540d290135b5f2f7fe5a4bd1086a57119968fc16af7716",
  "_filesize": 388399,
  "_sha256": "f5861e3700516f00e1540d290135b5f2f7fe5a4bd1086a57119968fc16af7716",
  "_created": "2026-05-20T09:48:51.000Z",
  "_published": "2026-06-02T13:19:42.525Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79079692251,
      "time": 252,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7106797561"
    },
    {
      "job": 79079692329,
      "time": 251,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7106797246"
    },
    {
      "job": 79079692499,
      "time": 152,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7106761830"
    },
    {
      "job": 79079692203,
      "time": 176,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7106770764"
    },
    {
      "job": 79079692349,
      "time": 251,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7106706721"
    },
    {
      "job": 79079691453,
      "time": 178,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7358802061"
    },
    {
      "job": 79079692258,
      "time": 213,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7106784671"
    },
    {
      "job": 79079692383,
      "time": 224,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7106787753"
    },
    {
      "job": 79079692292,
      "time": 176,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7106771202"
    }
  ],
  "_buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/igordot/scooter",
  "_commit": {
    "id": "2a639459d3848e111717624497797441cfbf1747",
    "author": "igor <6363505+igordot@users.noreply.github.com>",
    "committer": "igor <6363505+igordot@users.noreply.github.com>",
    "message": "Update pkgdown\n",
    "time": 1700258998
  },
  "_maintainer": {
    "name": "Igor Dolgalev",
    "email": "igor.dolgalev@nyumc.org",
    "login": "igordot",
    "description": "",
    "uuid": 6363505
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggsci",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "sctransform",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "version": ">= 4.0.2",
      "role": "Imports"
    },
    {
      "package": "SeuratObject",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "igordot",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "ayeaton",
      "count": 71,
      "uuid": 16885940
    },
    {
      "user": "igordot",
      "count": 51,
      "uuid": 6363505
    }
  ],
  "_userbio": {
    "uuid": 6363505,
    "type": "user",
    "name": "igor"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scooter"
  },
  "_devurl": "https://github.com/igordot/scooter",
  "_searchresults": 79,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/scooter.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    ".data",
    "%>%",
    "add_seurat_assay",
    "as_data_frame_seurat",
    "calc_clust_averages",
    "calculate_clusters",
    "calculate_mito_pct",
    "calculate_variance",
    "check_identity_column",
    "create_color_vect",
    "create_seurat_obj",
    "differential_expression_per_cluster",
    "enexpr",
    "enexprs",
    "enquo",
    "enquos",
    "ensym",
    "ensyms",
    "expr",
    "filter_data",
    "geneset_score",
    "get_color_scheme",
    "get_dr_point_size",
    "get_test_counts_matrix",
    "import_mtx",
    "load_sample_counts_matrix",
    "log_normalize_data",
    "merge_metadata",
    "normalize_data",
    "plot_distribution",
    "quo",
    "quo_name",
    "quos",
    "run_dr",
    "run_pca",
    "run_tsne",
    "run_umap",
    "save_seurat_counts_matrix",
    "sctransform_data",
    "set_identity",
    "sym",
    "syms",
    "write_message"
  ],
  "_help": [
    {
      "page": "add_seurat_assay",
      "title": "Add assay to Seurat object.",
      "topics": [
        "add_seurat_assay"
      ]
    },
    {
      "page": "as_data_frame_seurat",
      "title": "Function to extract data from Seurat object.",
      "topics": [
        "as_data_frame_seurat"
      ]
    },
    {
      "page": "calc_clust_averages",
      "title": "Get cluster averages.",
      "topics": [
        "calc_clust_averages"
      ]
    },
    {
      "page": "calculate_clusters",
      "title": "Run dimensionality reduction, pca, tse, and umap",
      "topics": [
        "calculate_clusters"
      ]
    },
    {
      "page": "calculate_mito_pct",
      "title": "Calculate mitochondrial percentage from Seurat object.",
      "topics": [
        "calculate_mito_pct"
      ]
    },
    {
      "page": "calculate_variance",
      "title": "Get variable genes and scale data.",
      "topics": [
        "calculate_variance"
      ]
    },
    {
      "page": "check_identity_column",
      "title": "Check identity of the Seurat object.",
      "topics": [
        "check_identity_column"
      ]
    },
    {
      "page": "create_color_vect",
      "title": "Function to create a color vector.",
      "topics": [
        "create_color_vect"
      ]
    },
    {
      "page": "create_seurat_obj",
      "title": "Create a new Seurat object from a matrix.",
      "topics": [
        "create_seurat_obj"
      ]
    },
    {
      "page": "differential_expression_global",
      "title": "Calculate differential expression for one group versus all",
      "topics": [
        "differential_expression_global"
      ]
    },
    {
      "page": "differential_expression_paired",
      "title": "Calculate differential expression between specific groups",
      "topics": [
        "differential_expression_paired"
      ]
    },
    {
      "page": "differential_expression_per_cluster",
      "title": "Calculate differentially expressed genes within each subpopulation/cluster",
      "topics": [
        "differential_expression_per_cluster"
      ]
    },
    {
      "page": "filter_data",
      "title": "Filter cells based on the number of genes and mitochondrial reads.",
      "topics": [
        "filter_data"
      ]
    },
    {
      "page": "geneset_score",
      "title": "Get geneset scores.",
      "topics": [
        "geneset_score"
      ]
    },
    {
      "page": "get_color_scheme",
      "title": "Determine the color scheme.",
      "topics": [
        "get_color_scheme"
      ]
    },
    {
      "page": "get_dr_point_size",
      "title": "Determine the point size for reduced dimensions scatter plots (smaller for larger datasets).",
      "topics": [
        "get_dr_point_size"
      ]
    },
    {
      "page": "get_test_counts_matrix",
      "title": "Get an example counts matrix.",
      "topics": [
        "get_test_counts_matrix"
      ]
    },
    {
      "page": "import_mtx",
      "title": "Read in 10x Genomics Cell Ranger Matrix Market format data.",
      "topics": [
        "import_mtx"
      ]
    },
    {
      "page": "load_sample_counts_matrix",
      "title": "Read in Gene Expression and Antibody Capture data from a 10x Genomics Cell Ranger sparse matrix or from a text file.",
      "topics": [
        "load_sample_counts_matrix"
      ]
    },
    {
      "page": "log_normalize_data",
      "title": "Log normalize data.",
      "topics": [
        "log_normalize_data"
      ]
    },
    {
      "page": "merge_metadata",
      "title": "Function to merge two metadata tables together.",
      "topics": [
        "merge_metadata"
      ]
    },
    {
      "page": "normalize_data",
      "title": "Normalize data",
      "topics": [
        "normalize_data"
      ]
    },
    {
      "page": "plot_distribution",
      "title": "Plot the distribution of specified features/variables.",
      "topics": [
        "plot_distribution"
      ]
    },
    {
      "page": "run_dr",
      "title": "Run dimensionality reduction, pca, tse, and umap",
      "topics": [
        "run_dr"
      ]
    },
    {
      "page": "run_pca",
      "title": "Run PCA",
      "topics": [
        "run_pca"
      ]
    },
    {
      "page": "run_tsne",
      "title": "Run TSNE",
      "topics": [
        "run_tsne"
      ]
    },
    {
      "page": "run_umap",
      "title": "Run UMAP",
      "topics": [
        "run_umap"
      ]
    },
    {
      "page": "save_seurat_counts_matrix",
      "title": "Function to write Seurat counts matrix to csv.",
      "topics": [
        "save_seurat_counts_matrix"
      ]
    },
    {
      "page": "sctransform_data",
      "title": "SCT normalize data.",
      "topics": [
        "sctransform_data"
      ]
    },
    {
      "page": "set_identity",
      "title": "Set identity of the Seurat object.",
      "topics": [
        "set_identity"
      ]
    },
    {
      "page": "write_message",
      "title": "Small function to write to message and to log file.",
      "topics": [
        "write_message"
      ]
    }
  ],
  "_readme": "https://github.com/igordot/scooter/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "BH",
    "bit",
    "bit64",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "deldir",
    "digest",
    "dotCall64",
    "dplyr",
    "dqrng",
    "evaluate",
    "farver",
    "fastDummies",
    "fastmap",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "ggrepel",
    "ggridges",
    "ggsci",
    "globals",
    "glue",
    "goftest",
    "gplots",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "igraph",
    "irlba",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nlme",
    "openssl",
    "otel",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "prettyunits",
    "progress",
    "progressr",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppTOML",
    "readr",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rprojroot",
    "RSpectra",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "sctransform",
    "Seurat",
    "SeuratObject",
    "shiny",
    "sitmo",
    "sourcetools",
    "sp",
    "spam",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tensor",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "zoo"
  ],
  "_score": 3.3747483460101035,
  "_indexed": true,
  "_nocasepkg": "scooter",
  "_universes": [
    "igordot"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:51:58.000Z",
      "distro": "noble",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "0ae9d787140a766f1fb36a93a48319699c0ad9d2bf7926af44f8b4aa1745a7e1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:52:01.000Z",
      "distro": "noble",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "2ed10a946834ba9363c34fa33445c916b24154ee015fb22b1530d29372204334",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:50:42.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "e8bfd3af2bbbbc7af373e7fc05c32d4dfe8c3352dcff8387b964d338e5c8cf14",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:50:58.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "b344b0dca807aa2979a7d7d5ee1c1a1f54e01fb76d68872c8d55fe5778de43ed",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:51:07.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "dc64155359a65befb55a422c806b951553e952f94a23a6fcdf707773acc23553",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:51:07.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "c83c00134ee55cc4731c87ef7cc2e80ddb0b115a2b8d83d8ec028c419f75b072",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9004",
      "date": "2026-05-20T09:50:32.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "e176fd1ef6a9366cd60cdccc8e186c6f25c3a2f9635d38e9d5fe5bd206ee5fd4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.0.9004",
      "date": "2026-06-02T13:19:08.000Z",
      "commit": "2a639459d3848e111717624497797441cfbf1747",
      "fileid": "441db0173ab46c20839e7c1b77eb36a4085c167bdbf20065b495e9e0bcb27849",
      "status": "success",
      "buildurl": "https://github.com/r-universe/igordot/actions/runs/26154621681"
    }
  ]
}