{
  "_id": "6a1aa9331d7bb097a09d4cb9",
  "Package": "RNAseqCovarImpute",
  "Title": "Impute Covariate Data in RNA Sequencing Studies",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(\"Brennan\", \"Baker\", email = \"brennanhilton@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5459-9141\")),\nperson(\"Sheela\", \"Sathyanarayana\", role = \"aut\"),\nperson(\"Adam\", \"Szpiro\", role = \"aut\"),\nperson(\"James\", \"MacDonald\", role = \"aut\"),\nperson(\"Alison\", \"Paquette\", role = \"aut\"))",
  "URL": "https://github.com/brennanhilton/RNAseqCovarImpute",
  "BugReports": "https://github.com/brennanhilton/RNAseqCovarImpute/issues",
  "Description": "The RNAseqCovarImpute package makes linear model analysis\nfor RNA sequencing read counts compatible with multiple\nimputation (MI) of missing covariates. A major problem with\nimplementing MI in RNA sequencing studies is that the outcome\ndata must be included in the imputation prediction models to\navoid bias. This is difficult in omics studies with\nhigh-dimensional data. The first method we developed in the\nRNAseqCovarImpute package surmounts the problem of\nhigh-dimensional outcome data by binning genes into smaller\ngroups to analyze pseudo-independently. This method implements\ncovariate MI in gene expression studies by 1) randomly binning\ngenes into smaller groups, 2) creating M imputed datasets\nseparately within each bin, where the imputation predictor\nmatrix includes all covariates and the log counts per million\n(CPM) for the genes within each bin, 3) estimating gene\nexpression changes using `limma::voom` followed by\n`limma::lmFit` functions, separately on each M imputed dataset\nwithin each gene bin, 4) un-binning the gene sets and stacking\nthe M sets of model results before applying the\n`limma::squeezeVar` function to apply a variance shrinking\nBayesian procedure to each M set of model results, 5) pooling\nthe results with Rubins’ rules to produce combined\ncoefficients, standard errors, and P-values, and 6) adjusting\nP-values for multiplicity to account for false discovery rate\n(FDR). A faster method uses principal component analysis (PCA)\nto avoid binning genes while still retaining outcome\ninformation in the MI models. Binning genes into smaller groups\nrequires that the MI and limma-voom analysis is run many times\n(typically hundreds). The more computationally efficient MI PCA\nmethod implements covariate MI in gene expression studies by 1)\nperforming PCA on the log CPM values for all genes using the\nBioconductor `PCAtools` package, 2) creating M imputed datasets\nwhere the imputation predictor matrix includes all covariates\nand the optimum number of PCs to retain (e.g., based on Horn’s\nparallel analysis or the number of PCs that account for >80%\nexplained variation), 3) conducting the standard limma-voom\npipeline with the `voom` followed by `lmFit` followed by\n`eBayes` functions on each M imputed dataset, 4) pooling the\nresults with Rubins’ rules to produce combined coefficients,\nstandard errors, and P-values, and 5) adjusting P-values for\nmultiplicity to account for false discovery rate (FDR).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "biocViews": "RNASeq, GeneExpression, DifferentialExpression, Sequencing",
  "Config/testthat/edition": "3",
  "Collate": "'RNAseqCovarImpute-package.R' 'combine_rubins.R'\n'combine_rubins_pca.R' 'example_DGE.R' 'example_data.R'\n'get_gene_bin_intervals.R' 'impute_by_gene_bin_helper.R'\n'impute_by_gene_bin.R' 'voom_sx_sy.R' 'lowess_all_gene_bins.R'\n'voom_master_lowess.R' 'limmavoom_imputed_data_list_helper.R'\n'limmavoom_imputed_data_list.R'\n'limmavoom_imputed_data_pca_helper.R'\n'limmavoom_imputed_data_pca.R'",
  "Config/pak/sysreqs": "cmake make libicu-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:45 UTC",
  "RemoteUrl": "https://github.com/bioc/RNAseqCovarImpute",
  "RemoteRef": "HEAD",
  "RemoteSha": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 06:54:49 UTC",
    "User": "root"
  },
  "Author": "Brennan Baker [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5459-9141>),\nSheela Sathyanarayana [aut],\nAdam Szpiro [aut],\nJames MacDonald [aut],\nAlison Paquette [aut]",
  "Maintainer": "Brennan Baker <brennanhilton@gmail.com>",
  "MD5sum": "027730ac0e4c6bc02d8f5579d8b47692",
  "_user": "bioc",
  "_type": "src",
  "_file": "RNAseqCovarImpute_1.11.0.tar.gz",
  "_fileid": "07d8cc5cea8114e2204f8b88a8cf80d299c14b482f2c931a95d50df8e8f20fbc",
  "_filesize": 468843,
  "_sha256": "07d8cc5cea8114e2204f8b88a8cf80d299c14b482f2c931a95d50df8e8f20fbc",
  "_created": "2026-05-30T06:54:49.000Z",
  "_published": "2026-05-30T09:09:07.828Z",
  "_jobs": [
    {
      "job": 78631693589,
      "time": 220,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306262966"
    },
    {
      "job": 78631693586,
      "time": 285,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306270604"
    },
    {
      "job": 78631693593,
      "time": 272,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306270163"
    },
    {
      "job": 78631693590,
      "time": 121,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307059210"
    },
    {
      "job": 78631693582,
      "time": 159,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307061913"
    },
    {
      "job": 78631472666,
      "time": 252,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306238605"
    },
    {
      "job": 78631693581,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306256702"
    },
    {
      "job": 78631693594,
      "time": 241,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306265556"
    },
    {
      "job": 78631693598,
      "time": 220,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306262876"
    },
    {
      "job": 78631693588,
      "time": 283,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306270243"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677323256",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RNAseqCovarImpute",
  "_commit": {
    "id": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
    "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": 1777381305
  },
  "_maintainer": {
    "name": "Brennan Baker",
    "email": "brennanhilton@gmail.com",
    "login": "brennanhilton",
    "description": "",
    "uuid": 42975032,
    "orcid": "0000-0001-5459-9141"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "mice",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "PCAtools",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "rnaseq",
    "geneexpression",
    "differentialexpression",
    "sequencing"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "brennanhilton",
      "count": 51,
      "uuid": 42975032
    },
    {
      "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": 242,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RNAseqCovarImpute"
  },
  "_devurl": "https://github.com/brennanhilton/rnaseqcovarimpute",
  "_searchresults": 11,
  "_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/RNAseqCovarImpute.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/brennanhilton/rnaseqcovarimpute",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "combine_rubins",
    "get_gene_bin_intervals",
    "impute_by_gene_bin",
    "limmavoom_imputed_data_list",
    "limmavoom_imputed_data_pca"
  ],
  "_datasets": [
    {
      "name": "example_data",
      "title": "Simulated dataset",
      "object": "example_data",
      "file": "example_data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x",
        "y",
        "z",
        "a",
        "b"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_DGE",
      "title": "Simulated counts in DGE list",
      "object": "example_DGE",
      "file": "example_DGE.rda",
      "class": [
        "DGEList"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "combine_rubins",
      "title": "combine_rubins",
      "topics": [
        "combine_rubins"
      ]
    },
    {
      "page": "example_data",
      "title": "Simulated dataset",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "example_DGE",
      "title": "Simulated counts in DGE list",
      "topics": [
        "example_DGE"
      ]
    },
    {
      "page": "get_gene_bin_intervals",
      "title": "get_gene_bin_intervals",
      "topics": [
        "get_gene_bin_intervals"
      ]
    },
    {
      "page": "impute_by_gene_bin",
      "title": "impute_by_gene_bin",
      "topics": [
        "impute_by_gene_bin"
      ]
    },
    {
      "page": "limmavoom_imputed_data_list",
      "title": "limmavoom_imputed_data_list",
      "topics": [
        "limmavoom_imputed_data_list"
      ]
    },
    {
      "page": "limmavoom_imputed_data_pca",
      "title": "limmavoom_imputed_data_pca",
      "topics": [
        "limmavoom_imputed_data_pca"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RNAseqCovarImpute/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "boot",
    "broom",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "dplyr",
    "edgeR",
    "forcats",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "glmnet",
    "glue",
    "haven",
    "hms",
    "iterators",
    "jomo",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "lme4",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "mice",
    "minqa",
    "mitml",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "ordinal",
    "pan",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rbibutils",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "rpart",
    "shape",
    "snow",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "ucminf",
    "utf8",
    "vctrs",
    "vroom",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Example_Data_for_RNAseqCovarImpute.Rmd",
      "filename": "Example_Data_for_RNAseqCovarImpute.html",
      "title": "Example Data for RNAseqCovarImpute",
      "author": "Brennan H Baker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Generate random data",
        "Simulate missingness in the random data",
        "Session info"
      ],
      "created": "2023-03-16 20:17:50",
      "modified": "2023-10-03 23:50:52",
      "commits": 2
    },
    {
      "source": "Impute_Covariate_Data_in_RNA_sequencing_Studies.Rmd",
      "filename": "Impute_Covariate_Data_in_RNA_sequencing_Studies.html",
      "title": "Impute Covariate Data in RNA-sequencing Studies",
      "author": "Brennan H Baker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Generate random data with missing covariate data",
        "RNAseqCovarImpute Demonstration",
        "MI PCA method",
        "Conduct PCA",
        "Conduct MI with mice",
        "Conduct limma-voom analysis",
        "Adjust for FDR",
        "Gene binning MI method",
        "Bin the genes into smaller groups",
        "Make imputed data sets for each bin of genes and conduct differential expression analysis",
        "Estimate gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin",
        "Apply variance shrinking Bayesian procedure, pooling results with Rubins’ rules, and FDR-adjust P-values",
        "Session info"
      ],
      "created": "2023-03-09 23:57:47",
      "modified": "2024-04-12 21:35:55",
      "commits": 12
    }
  ],
  "_score": 4.342422680822207,
  "_indexed": true,
  "_nocasepkg": "rnaseqcovarimpute",
  "_universes": [
    "bioc",
    "brennanhilton"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-04-30T15:40:21.000Z",
      "distro": "noble",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "0b60acc09d558a6a4b9c102d9c84887702b2486144c67833a62a09c9880bf92b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-04-30T15:41:05.000Z",
      "distro": "noble",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "e1eb27210292ed8f88d35b06917bc4c9fd1c3ccb2bba2b1c2a6a2408debb99e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-04-30T17:11:55.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "0078f74e9b91069a7c9985d934407a922a9b32ab421e6fe6a1da559ef56b72a1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-04-30T17:11:44.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "0cdebc8e73f3fa6606da79457d67bcffe650c400607ab0eae4e016efc26014ff",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-04-30T15:37:57.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "bf1e48fb30dd6b86974b4d12cf90c96324f1d060aab4bc84626322636b154089",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-04-30T15:41:35.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "cf588ff8dba05b65a5d17f03ead14495441decd14462c4fed5ec7e7250e424ba",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-04-30T15:37:41.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "0fcab37911932eee95cc2150ecc93d07d84356301ef350e96b1a7c7c12908424",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-05-22T21:04:16.000Z",
      "commit": "3ddac52327da56f5a7f8dad9e8c5bb4ef3ca938b",
      "fileid": "c3984e430568f3132238c1ab2772c0fd4a58618f20313bbb738bbd5ab9af385b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173722863"
    }
  ]
}