{
  "_id": "6a4b4702a6574ff277f98df8",
  "Package": "bayNorm",
  "Type": "Package",
  "Title": "Single-cell RNA sequencing data normalization",
  "Version": "1.31.0",
  "Authors@R": "c(person(\"Wenhao\", \"Tang\", role=c(\"aut\", \"cre\"),\nemail=\"wt215@ic.ac.uk\"),\nperson(\"Fran<U+00E7>ois\", \"Bertaux\", role=c(\"aut\")),\nperson(\"Philipp\", \"Thomas\", role=c(\"aut\")),\nperson(\"Claire\", \"Stefanelli\", role=c(\"aut\")),\nperson(\"Malika\", \"Saint\", role=c(\"aut\")),\nperson(\"Samuel\", \"Marguerat\", role=c(\"aut\")),\nperson(\"Vahid\", \"Shahrezaei\", role=c(\"aut\")))",
  "Description": "bayNorm is used for normalizing single-cell RNA-seq data.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.0.2",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, Normalization, RNASeq, SingleCell,Sequencing",
  "URL": "https://github.com/WT215/bayNorm",
  "BugReports": "https://github.com/WT215/bayNorm/issues",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:53 UTC",
  "RemoteUrl": "https://github.com/bioc/bayNorm",
  "RemoteRef": "HEAD",
  "RemoteSha": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 08:50:19 UTC",
    "User": "root"
  },
  "Author": "Wenhao Tang [aut, cre],\nFran<U+00E7>ois Bertaux [aut],\nPhilipp Thomas [aut],\nClaire Stefanelli [aut],\nMalika Saint [aut],\nSamuel Marguerat [aut],\nVahid Shahrezaei [aut]",
  "Maintainer": "Wenhao Tang <wt215@ic.ac.uk>",
  "_user": "bioc",
  "_type": "src",
  "_file": "bayNorm_1.31.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/5287f984eb140340ef7308a91ff5b42e7d19a82ede6cc71f90494e7ffe52628a",
  "_filesize": 1554918,
  "_sha256": "5287f984eb140340ef7308a91ff5b42e7d19a82ede6cc71f90494e7ffe52628a",
  "_expires": "2026-10-12T17:24:22.000Z",
  "_created": "2026-07-04T08:50:19.000Z",
  "_published": "2026-07-06T06:11:14.204Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955",
  "_status": "success",
  "_upstream": "https://github.com/bioc/bayNorm",
  "_commit": {
    "id": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
    "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": 1777380533
  },
  "_maintainer": {
    "name": "Wenhao Tang",
    "email": "wt215@ic.ac.uk"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85304667172,
      "time": 217,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080215088"
    },
    {
      "job": 85304667132,
      "time": 276,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8080222476"
    },
    {
      "job": 85304667119,
      "time": 370,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8080233721"
    },
    {
      "job": 85304667364,
      "time": 275,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080222329"
    },
    {
      "job": 85304667330,
      "time": 405,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080238283"
    },
    {
      "job": 85304666817,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 85304666833,
      "time": 195,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 85304667182,
      "time": 233,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080456024"
    },
    {
      "job": 85304667238,
      "time": 355,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080233341"
    },
    {
      "job": 85304666836,
      "time": 319,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8080189669"
    },
    {
      "job": 85304667079,
      "time": 199,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8080213010"
    },
    {
      "job": 85304667016,
      "time": 259,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8080220102"
    },
    {
      "job": 85304666788,
      "time": 95,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 85304667213,
      "time": 266,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8080220872"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "RcppProgress",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.12",
      "role": "Imports"
    },
    {
      "package": "BB",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "doSNOW",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "locfit",
      "role": "Imports"
    },
    {
      "package": "fitdistrplus",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "normalization",
    "rnaseq",
    "singlecell",
    "sequencing",
    "scrnaseq",
    "cpp",
    "openmp"
  ],
  "_stars": 10,
  "_contributors": [
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "vshahrez",
      "count": 3,
      "uuid": 14345790
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/wt215/baynorm",
  "_searchresults": 39,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bayNorm.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wt215/baynorm",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AdjustSIZE_fun",
    "as_matrix",
    "asMatrix",
    "bayNorm",
    "bayNorm_sup",
    "BB_Fun",
    "BetaFun",
    "Check_input",
    "DownSampling",
    "EstPrior",
    "EstPrior_rcpp",
    "EstPrior_sprcpp",
    "NOISY_FUN",
    "noisy_gene_detection",
    "Prior_fun",
    "SyntheticControl",
    "t_sp"
  ],
  "_datasets": [
    {
      "name": "EXAMPLE_DATA_list",
      "title": "A subset of Grun et al (2014) data: 2i samples",
      "object": "EXAMPLE_DATA_list",
      "file": "EXAMPLE_DATA_list.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AdjustSIZE_fun",
      "title": "Adjust MME size estimate",
      "topics": [
        "AdjustSIZE_fun"
      ]
    },
    {
      "page": "as_matrix",
      "title": "Rcpp version's as.matrix",
      "topics": [
        "as_matrix"
      ]
    },
    {
      "page": "asMatrix",
      "title": "Rcpp version: as.matrix",
      "topics": [
        "asMatrix"
      ]
    },
    {
      "page": "bayNorm",
      "title": "A wrapper function of prior estimation and bayNorm function",
      "topics": [
        "bayNorm"
      ]
    },
    {
      "page": "bayNorm_sup",
      "title": "bayNorm with estimated parameters as input",
      "topics": [
        "bayNorm_sup"
      ]
    },
    {
      "page": "BB_Fun",
      "title": "Estimating size for each gene by either 1D or 2D maximization of marginal distribution",
      "topics": [
        "BB_Fun"
      ]
    },
    {
      "page": "BetaFun",
      "title": "Estimate capture efficiency for cells",
      "topics": [
        "BetaFun"
      ]
    },
    {
      "page": "Check_input",
      "title": "Check input",
      "topics": [
        "Check_input"
      ]
    },
    {
      "page": "DownSampling",
      "title": "Binomial downsampling",
      "topics": [
        "DownSampling"
      ]
    },
    {
      "page": "EstPrior",
      "title": "Estimate size and mu for Negative Binomial distribution for each gene using MME method",
      "topics": [
        "EstPrior"
      ]
    },
    {
      "page": "EstPrior_rcpp",
      "title": "Estimate size and mu for Negative Binomial distribution for each gene using MME method (Rcpp version)",
      "topics": [
        "EstPrior_rcpp"
      ]
    },
    {
      "page": "EstPrior_sprcpp",
      "title": "Estimate size and mu for Negative Binomial distribution for each gene using MME method (Rcpp version, sp_mat)",
      "topics": [
        "EstPrior_sprcpp"
      ]
    },
    {
      "page": "EXAMPLE_DATA_list",
      "title": "A subset of Grun et al (2014) data: 2i samples",
      "topics": [
        "EXAMPLE_DATA_list"
      ]
    },
    {
      "page": "NOISY_FUN",
      "title": "Noisy gene detection",
      "topics": [
        "NOISY_FUN"
      ]
    },
    {
      "page": "noisy_gene_detection",
      "title": "A wrapper function for noisy gene detection from raw data. his produces synthetic control, performs bayNorm on both real cell data and synthetic controls and does noisy gene detection.",
      "topics": [
        "noisy_gene_detection"
      ]
    },
    {
      "page": "Prior_fun",
      "title": "A wrapper function of 'EstPrior' and 'AdjustSIZE_fun'",
      "topics": [
        "Prior_fun"
      ]
    },
    {
      "page": "SyntheticControl",
      "title": "Generate synthetic control",
      "topics": [
        "SyntheticControl"
      ]
    },
    {
      "page": "t_sp",
      "title": "Transpose of sparse matrix",
      "topics": [
        "t_sp"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/bayNorm/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BB",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "codetools",
    "cpp11",
    "DelayedArray",
    "doSNOW",
    "fitdistrplus",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "IRanges",
    "iterators",
    "lambda.r",
    "lattice",
    "locfit",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "quadprog",
    "Rcpp",
    "RcppArmadillo",
    "RcppProgress",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "survival",
    "XVector"
  ],
  "_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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "bayNorm.Rmd",
      "filename": "bayNorm.html",
      "title": "Introduction to bayNorm",
      "author": "Wenhao Tang, Fran<U+00E7>ois Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Quick start: for either one or multi groups of cells",
        "Estimation of capture efficiencies",
        "Run bayNorm",
        "Non-UMI scRNAseq dataset",
        "Generate 3D array or 2D matrix with existing estimated prior parameters.",
        "Other functions",
        "Methods",
        "Rationale of bayNorm",
        "Estimation of prior parameters",
        "Maximisation of marginal distribution",
        "Method of Moments",
        "The combined method (default setting in bayNorm for estimating priors)",
        "Session information",
        "References"
      ],
      "created": "2017-12-11 17:00:23",
      "modified": "2019-03-26 15:51:26",
      "commits": 17
    }
  ],
  "_score": 6.545307116465824,
  "_indexed": true,
  "_nocasepkg": "baynorm",
  "_universes": [
    "bioc",
    "wt215"
  ],
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-04-09T08:31:12.000Z",
      "arch": "aarch64",
      "commit": "afe0e446143fd00bf47ab5cab876a27b8e8bd2c8",
      "fileid": "https://r2.ropensci.org/4b910229a4a87b822077819922c485fbd93dff239e3b1d3d6ec81d8a67750d4f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24180189529"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-04-09T08:31:08.000Z",
      "arch": "x86_64",
      "commit": "afe0e446143fd00bf47ab5cab876a27b8e8bd2c8",
      "fileid": "https://r2.ropensci.org/c10e4beb23d4c8aa5d1eae003f9338bad3c6e73407e4bdf7111df2d41f0d0aa1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24180189529"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-04-09T08:28:12.000Z",
      "arch": "x86_64",
      "commit": "afe0e446143fd00bf47ab5cab876a27b8e8bd2c8",
      "fileid": "https://r2.ropensci.org/b566822613379ef5a648863a608febbe0451c69603b1effb3d151bedec6ae7ec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24180189529"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T08:54:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/a850deb83b5c77a15036f791a48df36c4155643f5901fe1749062e29ada00cfd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T08:54:51.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/e2a99d0aad634288b839d0407446eab5a519e6b8016478f27de1760c4d55a1e2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T08:53:58.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/18b3fe210647522998277fa0d2241debc3c36fc97a15d89358ae97fafc1f652e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-07-04T08:55:24.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/a0dd902465395e5a7745aa2a58614cad701b6cf9c62bd69006300d175ee9b93b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T09:26:10.000Z",
      "arch": "aarch64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/1590f46592efc0d21ab5cecabe4f94f355ab9292ac5fa66a32e591145934481c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-07-04T08:54:18.000Z",
      "arch": "x86_64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/9966ee1c062b7ac691f56a17dc028f83a09dc7a5ebab996dad5a1dd6bd37210a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-07-04T08:54:13.000Z",
      "arch": "emscripten",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/baf9cb0081cf599b4ae03b3168a694b85214cf64c3fd4c83c8f47449893d326c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-04T08:52:31.000Z",
      "arch": "x86_64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/2f073049118afd9b94185a85c17fc6f312f15bcabb61e6f9c937a1b1bb248e04",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-07-04T08:52:34.000Z",
      "arch": "x86_64",
      "commit": "6b1aefc1f83d9585bc8bc2b566da4aa3670d75ed",
      "fileid": "https://r2.ropensci.org/1c4f2a1fb98ac78a1d2fe1e40ca111991790e3c268e4d05ea9882184ea09b9a0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700931955"
    }
  ]
}