{
  "_id": "6a0f6918acfb0bcc41c5dd3b",
  "Package": "RNAseqQC",
  "Title": "Quality Control for RNA-Seq Data",
  "Version": "0.2.1.9000",
  "Authors@R": "c(\nperson(\"Frederik\", \"Ziebell\", email=\"f_ziebell@web.de\", role = \"cre\"),\nperson(\"Frederik\", \"Ziebell\", email=\"frederik.x.ziebell@gsk.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-3673-1721\")),\nperson(\"GlaxoSmithKline Research & Development Limited\", role = \"cph\", comment = \"GlaxoSmithKline Research & Development Limited; registered address: 980 Great West Road, Brentford, Middlesex TW8 9GS, United Kingdom\")\n)",
  "Description": "Functions for semi-automated quality control of bulk\nRNA-seq data.",
  "License": "Apache License (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/frederikziebell/RNAseqQC",
  "BugReports": "https://github.com/frederikziebell/RNAseqQC/issues",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev perl xz-utils zlib1g-dev",
  "Repository": "https://frederikziebell.r-universe.dev",
  "Date/Publication": "2026-02-16 13:32:36 UTC",
  "RemoteUrl": "https://github.com/frederikziebell/rnaseqqc",
  "RemoteRef": "HEAD",
  "RemoteSha": "d38839a48418815bca899a6bb76f8a49f9c7789d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-21 09:00:00 UTC",
    "User": "root"
  },
  "Author": "Frederik Ziebell [cre],\nFrederik Ziebell [aut] (ORCID: <https://orcid.org/0000-0003-3673-1721>),\nGlaxoSmithKline Research & Development Limited [cph] (GlaxoSmithKline\nResearch & Development Limited; registered address: 980 Great West\nRoad, Brentford, Middlesex TW8 9GS, United Kingdom)",
  "Maintainer": "Frederik Ziebell <f_ziebell@web.de>",
  "MD5sum": "11d94c79546856803f15efd33f4ac39d",
  "_user": "frederikziebell",
  "_type": "src",
  "_file": "RNAseqQC_0.2.1.9000.tar.gz",
  "_fileid": "73e4a205f9dc7ff3c887849a75704f5c5bb2a18dfb405bc428c0f2160d781c62",
  "_filesize": 5653342,
  "_sha256": "73e4a205f9dc7ff3c887849a75704f5c5bb2a18dfb405bc428c0f2160d781c62",
  "_created": "2026-05-21T09:00:00.000Z",
  "_published": "2026-05-21T20:20:40.320Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77260806327,
      "time": 331,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7131653323"
    },
    {
      "job": 77260806326,
      "time": 350,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7131659588"
    },
    {
      "job": 77260806427,
      "time": 265,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7131620421"
    },
    {
      "job": 77260806208,
      "time": 431,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7131667306"
    },
    {
      "job": 77260806116,
      "time": 314,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7131535581"
    },
    {
      "job": 77260805826,
      "time": 177,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7146293584"
    },
    {
      "job": 77260806475,
      "time": 221,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7131614002"
    },
    {
      "job": 77260806814,
      "time": 221,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7131614016"
    },
    {
      "job": 77260806433,
      "time": 269,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7131632179"
    }
  ],
  "_buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/frederikziebell/rnaseqqc",
  "_commit": {
    "id": "d38839a48418815bca899a6bb76f8a49f9c7789d",
    "author": "Frederik Ziebell <f_ziebell@web.de>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Add ECDF y-axis label",
    "time": 1771248756
  },
  "_maintainer": {
    "name": "Frederik Ziebell",
    "email": "f_ziebell@web.de",
    "login": "frederikziebell",
    "twitter": "@fredonion",
    "description": "Cyclist / Mathematician / Computational Biologist",
    "uuid": 28304028
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "AnnotationFilter",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "ensembldb",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "ggpointdensity",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "recount3",
      "role": "Suggests"
    },
    {
      "package": "apeglm",
      "role": "Suggests"
    },
    {
      "package": "ggrastr",
      "role": "Suggests"
    },
    {
      "package": "gghighlight",
      "role": "Suggests"
    }
  ],
  "_owner": "frederikziebell",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 2
    },
    {
      "week": "2026-08",
      "n": 3
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "frederikziebell",
      "count": 8,
      "uuid": 28304028
    }
  ],
  "_userbio": {
    "uuid": 28304028,
    "type": "user",
    "name": "Frederik Ziebell",
    "description": "Cyclist / Mathematician / Computational Biologist"
  },
  "_downloads": {
    "count": 314,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RNAseqQC"
  },
  "_devurl": "https://github.com/frederikziebell/rnaseqqc",
  "_searchresults": 92,
  "_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/RNAseqQC.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/frederikziebell/rnaseqqc",
  "_realowner": "frederikziebell",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2022-03-17"
    },
    {
      "version": "0.1.1",
      "date": "2022-03-18"
    },
    {
      "version": "0.1.2",
      "date": "2022-04-27"
    },
    {
      "version": "0.1.3",
      "date": "2022-05-27"
    },
    {
      "version": "0.1.4",
      "date": "2022-06-15"
    },
    {
      "version": "0.2.0",
      "date": "2024-07-01"
    },
    {
      "version": "0.2.1",
      "date": "2024-07-15"
    }
  ],
  "_exports": [
    "filter_genes",
    "get_gene_id",
    "make_dds",
    "mean_sd_plot",
    "plot_biotypes",
    "plot_chromosome",
    "plot_gene",
    "plot_gene_detection",
    "plot_library_complexity",
    "plot_loadings",
    "plot_ma",
    "plot_pca",
    "plot_pca_scatters",
    "plot_sample_boxplots",
    "plot_sample_clustering",
    "plot_sample_ecdfs",
    "plot_sample_MAs",
    "plot_total_counts",
    "plot_within_level_sample_MAs",
    "save_plots_to_pdf"
  ],
  "_datasets": [
    {
      "name": "T47D",
      "title": "The T47D cell line data of RNA-seq experiment GSE89888",
      "object": "T47D",
      "class": [
        "DESeqDataSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "T47D_diff_testing",
      "title": "Differential expression results corresponding to the T47D data set.",
      "object": "T47D_diff_testing",
      "class": [
        "DESeqResults"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "all_numeric",
      "title": "for a vector x, check if all non-NA elements of x can be converted to numeric",
      "topics": [
        "all_numeric"
      ]
    },
    {
      "page": "filter_genes",
      "title": "Filter genes with low counts",
      "topics": [
        "filter_genes"
      ]
    },
    {
      "page": "get_gene_id",
      "title": "Get all gene IDs in a DESeqDataSet for a given gene name.",
      "topics": [
        "get_gene_id"
      ]
    },
    {
      "page": "make_dds",
      "title": "Make DESeqDataSet from counts matrix and metadata",
      "topics": [
        "make_dds"
      ]
    },
    {
      "page": "mean_sd_plot",
      "title": "Create a mean-sd plot Make a scatterplot that shows for each gene its standard deviation versus mean.",
      "topics": [
        "mean_sd_plot"
      ]
    },
    {
      "page": "plot_biotypes",
      "title": "Plot number of counts per sample and biotype",
      "topics": [
        "plot_biotypes"
      ]
    },
    {
      "page": "plot_chromosome",
      "title": "Plot gene expression along a chromosome",
      "topics": [
        "plot_chromosome"
      ]
    },
    {
      "page": "plot_gene",
      "title": "Plot a gene",
      "topics": [
        "plot_gene"
      ]
    },
    {
      "page": "plot_gene_detection",
      "title": "Plot number of detected genes for each sample",
      "topics": [
        "plot_gene_detection"
      ]
    },
    {
      "page": "plot_library_complexity",
      "title": "Plot the library complexity",
      "topics": [
        "plot_library_complexity"
      ]
    },
    {
      "page": "plot_loadings",
      "title": "Plot loadings of a principal component",
      "topics": [
        "plot_loadings"
      ]
    },
    {
      "page": "plot_ma",
      "title": "MA-plot of a differential testing result",
      "topics": [
        "plot_ma"
      ]
    },
    {
      "page": "plot_pca",
      "title": "Plot results of a principal component analysis",
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_pca_scatters",
      "title": "Plot matrix of PCA scatter plots",
      "topics": [
        "plot_pca_scatters"
      ]
    },
    {
      "page": "plot_sample_boxplots",
      "title": "Plot one boxplot per sample",
      "topics": [
        "plot_sample_boxplots"
      ]
    },
    {
      "page": "plot_sample_clustering",
      "title": "Plot clustering of samples in a distance heatmap",
      "topics": [
        "plot_sample_clustering"
      ]
    },
    {
      "page": "plot_sample_ecdfs",
      "title": "Plot one ECDF per sample",
      "topics": [
        "plot_sample_ecdfs"
      ]
    },
    {
      "page": "plot_sample_MAs",
      "title": "MA plots of samples",
      "topics": [
        "plot_sample_MAs"
      ]
    },
    {
      "page": "plot_total_counts",
      "title": "Plot total counts per sample",
      "topics": [
        "plot_total_counts"
      ]
    },
    {
      "page": "plot_within_level_sample_MAs",
      "title": "Plot correlations of samples within a level of a group",
      "topics": [
        "plot_within_level_sample_MAs"
      ]
    },
    {
      "page": "save_plots_to_pdf",
      "title": "Save list of plots to PDF",
      "topics": [
        "save_plots_to_pdf"
      ]
    },
    {
      "page": "T47D",
      "title": "The T47D cell line data of RNA-seq experiment GSE89888",
      "topics": [
        "T47D"
      ]
    },
    {
      "page": "T47D_diff_testing",
      "title": "Differential expression results corresponding to the T47D data set.",
      "topics": [
        "T47D_diff_testing"
      ]
    }
  ],
  "_readme": "https://github.com/frederikziebell/rnaseqqc/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "AnnotationHub",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DESeq2",
    "digest",
    "doParallel",
    "dplyr",
    "ensembldb",
    "farver",
    "fastmap",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "ggpointdensity",
    "ggrepel",
    "GlobalOptions",
    "glue",
    "gtable",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "patchwork",
    "pillar",
    "pkgconfig",
    "png",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "data.Rmd",
      "filename": "data.html",
      "title": "Creating The Example Data Set",
      "author": "Frederik Ziebell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load Packages",
        "Download GSE89888 via recount3 and format data",
        "Differential testing"
      ],
      "created": "2024-06-21 17:44:51",
      "modified": "2024-06-21 18:06:01",
      "commits": 2
    },
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "RNA-seq Quality Control",
      "author": "Frederik Ziebell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Preparations",
        "Input data",
        "Create DESeqDataSet",
        "QC plots on raw count matrix",
        "Total sample counts",
        "Library complexity",
        "Gene detection",
        "Gene biotypes",
        "Gene filtering",
        "Variance stabilization",
        "Chromosomal expression",
        "Replicate variability",
        "Clustering",
        "PCA",
        "Differential expression",
        "Plot a gene",
        "Differential testing",
        "Plot a testing result",
        "SessionInfo"
      ],
      "created": "2024-06-21 17:44:51",
      "modified": "2024-06-21 18:06:01",
      "commits": 2
    }
  ],
  "_score": 5.7419390777291985,
  "_indexed": true,
  "_nocasepkg": "rnaseqqc",
  "_universes": [
    "frederikziebell"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:03:28.000Z",
      "distro": "noble",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "34ddc443f528f2b64481da6526894046f14af3fc8b5d97a17abf4fedb5987116",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:03:46.000Z",
      "distro": "noble",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "c1f27810acd0ade75146ce73606af900a5fcf5777ab57fc76e1962517d07390f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:02:54.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "99649d0d5d913fdd5e5ed3b128059d5034290eca94facfb7a96270b6894893c7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:03:12.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "f0396354d8ce8eff0912a36233887e0259f5deb1ac266bedcacaf98fc4c3d9f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.1.9000",
      "date": "2026-05-21T20:20:18.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "a6bb308c2ce30c18d04205a194e0dcb41a417d57e5a7c434e573a78c93e4ac47",
      "status": "success",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:01:47.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "58d0511f9d3adbec77dc35b6e5d3edb2b792e61e4046ff13cb4191667062306a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:01:51.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "a00e6b85de04df6fcfc5ab5be55b5014ecc9b966db574f153a2afd0d18ebce57",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.1.9000",
      "date": "2026-05-21T09:02:33.000Z",
      "commit": "d38839a48418815bca899a6bb76f8a49f9c7789d",
      "fileid": "4540fa5a859c63fa5d851fd85906307948680cd00fbee6fdd745f0f8a3810069",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/frederikziebell/actions/runs/26215986155"
    }
  ]
}