{
  "_id": "6a1b0bd31d7bb097a0a0763c",
  "Package": "scry",
  "Title": "Small-Count Analysis Methods for High-Dimensional Data",
  "Version": "1.24.0",
  "Description": "Many modern biological datasets consist of small counts\nthat are not well fit by standard linear-Gaussian methods such\nas principal component analysis. This package provides\nimplementations of count-based feature selection and dimension\nreduction algorithms. These methods can be used to facilitate\nunsupervised analysis of any high-dimensional data such as\nsingle-cell RNA-seq.",
  "Authors@R": "c(person(\"Kelly\", \"Street\", email = \"street.kelly@gmail.com\", \nrole = c(\"aut\", \"cre\")),\nperson(\"F. William\", \"Townes\", email = \"will.townes@gmail.com\",\nrole = c(\"aut\",  \"cph\")),\nperson(\"Davide\", \"Risso\", email = \"risso.davide@gmail.com\",\nrole = \"aut\"),\nperson(\"Stephanie\", \"Hicks\", email = \"shicks19@jhu.edu\",\nrole = \"aut\")\n)",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "URL": "https://bioconductor.org/packages/scry.html",
  "BugReports": "https://github.com/kstreet13/scry/issues",
  "RoxygenNote": "7.2.2",
  "Encoding": "UTF-8",
  "biocViews": "DimensionReduction, GeneExpression, Normalization,\nPrincipalComponent, RNASeq, Software, Sequencing, SingleCell,\nTranscriptomics",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:38 UTC",
  "RemoteUrl": "https://github.com/bioc/scry",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 11:02:22 UTC",
    "User": "root"
  },
  "Author": "Kelly Street [aut, cre],\nF. William Townes [aut, cph],\nDavide Risso [aut],\nStephanie Hicks [aut]",
  "Maintainer": "Kelly Street <street.kelly@gmail.com>",
  "MD5sum": "17a64e80441a8cfd84ecccbff89c2e40",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "scry_1.24.0.tar.gz",
  "_fileid": "e5f50523370cd177e68e7c4a706bb7ef8c60ea24a510ceaf212c117a85da2036",
  "_filesize": 5057163,
  "_sha256": "e5f50523370cd177e68e7c4a706bb7ef8c60ea24a510ceaf212c117a85da2036",
  "_created": "2026-05-30T11:02:22.000Z",
  "_published": "2026-05-30T16:09:55.573Z",
  "_jobs": [
    {
      "job": 78644376139,
      "time": 227,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307786178"
    },
    {
      "job": 78644376137,
      "time": 346,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307796980"
    },
    {
      "job": 78644376145,
      "time": 374,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307799519"
    },
    {
      "job": 78644376167,
      "time": 153,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309506357"
    },
    {
      "job": 78644376143,
      "time": 194,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309510074"
    },
    {
      "job": 78643835093,
      "time": 386,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307712160"
    },
    {
      "job": 78644376140,
      "time": 178,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307782529"
    },
    {
      "job": 78644376159,
      "time": 1107,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307863333"
    },
    {
      "job": 78644376166,
      "time": 933,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307846988"
    },
    {
      "job": 78644376161,
      "time": 1066,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307858738"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/scry",
  "_commit": {
    "id": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380758
  },
  "_maintainer": {
    "name": "Kelly Street",
    "email": "street.kelly@gmail.com",
    "login": "kstreet13",
    "description": "Assistant Professor of Population and Public Health Sciences, Division of Biostatistics",
    "uuid": 11052277
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "glmpca",
      "version": ">= 0.2.0",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "DuoClustering2018",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "HDF5Array",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "TENxPBMCData",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.24.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dimensionreduction",
    "geneexpression",
    "normalization",
    "principalcomponent",
    "rnaseq",
    "software",
    "sequencing",
    "singlecell",
    "transcriptomics"
  ],
  "_stars": 23,
  "_contributors": [
    {
      "user": "willtownes",
      "count": 60,
      "uuid": 810709
    },
    {
      "user": "kstreet13",
      "count": 11,
      "uuid": 11052277
    },
    {
      "user": "drisso",
      "count": 10,
      "uuid": 8451432
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "stephaniehicks",
      "count": 9,
      "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": 742,
    "source": "https://www.bioconductor.org/packages/stats/bioc/scry"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/kstreet13/scry",
  "_searchresults": 177,
  "_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/scry.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kstreet13/scry",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "devianceFeatureSelection",
    "GLMPCA",
    "nullResiduals"
  ],
  "_help": [
    {
      "page": "devianceFeatureSelection",
      "title": "Feature selection by approximate multinomial deviance",
      "topics": [
        "devianceFeatureSelection",
        "devianceFeatureSelection,DelayedArray-method",
        "devianceFeatureSelection,Matrix-method",
        "devianceFeatureSelection,matrix-method",
        "devianceFeatureSelection,SummarizedExperiment-method"
      ]
    },
    {
      "page": "GLMPCA",
      "title": "Generalized principal components analysis for non-normally distributed data",
      "topics": [
        "GLMPCA",
        "GLMPCA,Matrix-method",
        "GLMPCA,matrix-method",
        "GLMPCA,SummarizedExperiment-method"
      ]
    },
    {
      "page": "nullResiduals",
      "title": "Residuals from an approximate multinomial null model",
      "topics": [
        "nullResiduals",
        "nullResiduals,ANY-method",
        "nullResiduals,Matrix-method",
        "nullResiduals,matrix-method",
        "nullResiduals,SingleCellExperiment-method",
        "nullResiduals,SummarizedExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scry/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "BiocSingular",
    "codetools",
    "cpp11",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glmpca",
    "IRanges",
    "irlba",
    "lambda.r",
    "lattice",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "Rcpp",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "scry.Rmd",
      "filename": "scry.html",
      "title": "Overview of Scry Methods",
      "author": "Will Townes",
      "engine": "knitr::knitr",
      "headings": [
        "Basic Workflow",
        "Feature Selection with Deviance",
        "Dimension Reduction with GLM-PCA",
        "Dimension Reduction with Null Residuals"
      ],
      "created": "2020-04-21 21:51:51",
      "modified": "2020-10-13 05:02:38",
      "commits": 8
    },
    {
      "source": "bigdata.Rmd",
      "filename": "bigdata.html",
      "title": "Scry Methods For Larger Datasets",
      "author": "Will Townes",
      "engine": "knitr::knitr",
      "headings": [
        "Feature Selection with Deviance",
        "Null residuals"
      ],
      "created": "2020-08-27 00:03:18",
      "modified": "2020-10-13 05:02:38",
      "commits": 2
    }
  ],
  "_score": 8.086822357099063,
  "_indexed": false,
  "_nocasepkg": "scry",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/scry",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.24.0",
      "date": "2026-05-30T11:16:32.000Z",
      "distro": "noble",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "e2797b97a684c819f33f0c756e0c8dd22b09fa869890554407c6d4d7e85ebd10",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.24.0",
      "date": "2026-05-30T11:17:02.000Z",
      "distro": "noble",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "c3be8223514c77e4e00ca81add35a46a6fb6beaf5db2170d77ac420f428f43d0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.24.0",
      "date": "2026-05-30T16:07:53.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "cf282e3a46734321effecea5fae2765c4141606e361df94c4b7e7bd60271a475",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.24.0",
      "date": "2026-05-30T16:08:12.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "389e97343f428d22b3606167f23845f2ff7e218199d457aa963a4baab80965df",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.24.0",
      "date": "2026-05-30T11:15:57.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "73786228ab7f2816561df704eceea09c21083ddd35ee26d597ac35139b47c704",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T11:29:02.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "56668417d7312cc9d942c7027b7a9b1c51edcd420515f396dccf0437bf39c561",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T11:26:09.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "6182b0c6177e56ff2114de1da2e76bb08322e55de18e8394bfdc16658f791f6c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.24.0",
      "date": "2026-05-30T11:28:21.000Z",
      "commit": "f8a4dd94674c575bf45e8e1988503a9826c0225e",
      "fileid": "ab951fedf933ad0bd6f5d38448aec8ea9b3dbb6be226224410880f023ce5bf1c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680988487"
    }
  ]
}