{
  "_id": "6a10271facfb0bcc41c8fe5f",
  "Package": "noisyr",
  "Type": "Package",
  "Title": "Noise Quantification in High Throughput Sequencing Output",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\"Ilias\", \"Moutsopoulos\", , \"im383@cam.ac.uk\", c(\"aut\", \"cre\")),\nperson(\"Irina\", \"Mohorianu\", , \"iim22@cam.ac.uk\", role = c(\"aut\",\"ctb\")),\nperson(\"Hajk-Georg\", \"Drost\", , \"hajk-georg.drost@tuebingen.mpg.de\", role=\"ctb\"),\nperson(\"Elze\", \"Lauzikaite\", , \"el523@cam.ac.uk\", role = \"ctb\")\n)",
  "Maintainer": "Ilias Moutsopoulos <im383@cam.ac.uk>",
  "Description": "Quantifies and removes technical noise from\nhigh-throughput sequencing data. Two approaches are used, one\nbased on the count matrix, and one using the alignment BAM\nfiles directly. Contains several options for every step of the\nprocess, as well as tools to quality check and assess the\nstability of output.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "URL": "https://github.com/Core-Bioinformatics/noisyR",
  "BugReports": "https://github.com/Core-Bioinformatics/noisyR/issues",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev xz-utils zlib1g-dev",
  "Repository": "https://core-bioinformatics.r-universe.dev",
  "Date/Publication": "2021-10-01 11:55:21 UTC",
  "RemoteUrl": "https://github.com/core-bioinformatics/noisyr",
  "RemoteRef": "HEAD",
  "RemoteSha": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 08:44:37 UTC",
    "User": "root"
  },
  "Author": "Ilias Moutsopoulos [aut, cre],\nIrina Mohorianu [aut, ctb],\nHajk-Georg Drost [ctb],\nElze Lauzikaite [ctb]",
  "MD5sum": "586047ddc1b22e5e3d29342be3800211",
  "_user": "core-bioinformatics",
  "_type": "src",
  "_file": "noisyr_1.1.0.tar.gz",
  "_fileid": "3ddd6c968e68f2e1f6e6a3eb1e77a7373ce43e38f34da6928114f2242b47f9b0",
  "_filesize": 11180485,
  "_sha256": "3ddd6c968e68f2e1f6e6a3eb1e77a7373ce43e38f34da6928114f2242b47f9b0",
  "_created": "2026-05-13T08:44:37.000Z",
  "_published": "2026-05-22T09:51:27.871Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77356167711,
      "time": 191,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6965552383"
    },
    {
      "job": 77356167793,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6965538002"
    },
    {
      "job": 77356167736,
      "time": 111,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6965527465"
    },
    {
      "job": 77356167685,
      "time": 99,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6965523775"
    },
    {
      "job": 77356167237,
      "time": 258,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6965490732"
    },
    {
      "job": 77356167256,
      "time": 131,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157684596"
    },
    {
      "job": 77356167555,
      "time": 106,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "6965525975"
    },
    {
      "job": 77356167593,
      "time": 131,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "6965533927"
    },
    {
      "job": 77356167684,
      "time": 114,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6965528064"
    }
  ],
  "_buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/core-bioinformatics/noisyr",
  "_commit": {
    "id": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
    "author": "emouts <emouts@hotmail.com>",
    "committer": "emouts <emouts@hotmail.com>",
    "message": "Added UKCBCB slides\n",
    "time": 1633089321
  },
  "_maintainer": {
    "name": "Ilias Moutsopoulos",
    "email": "im383@cam.ac.uk"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.2",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "philentropy",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "core-bioinformatics",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 10,
  "_contributors": [
    {
      "user": "emouts",
      "count": 2,
      "uuid": 15875524
    }
  ],
  "_userbio": {
    "uuid": 71281163,
    "type": "organization",
    "name": "Core Bioinformatics group"
  },
  "_downloads": {
    "count": 217,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/noisyr"
  },
  "_devurl": "https://github.com/core-bioinformatics/noisyr",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/noisyr.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/core-bioinformatics/noisyr",
  "_realowner": "core-bioinformatics",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-01-06"
    },
    {
      "version": "1.0.0",
      "date": "2021-04-16"
    }
  ],
  "_exports": [
    "calculate_expression_profile",
    "calculate_expression_similarity_counts",
    "calculate_expression_similarity_transcript",
    "calculate_first_minimum_density",
    "calculate_noise_threshold",
    "calculate_noise_threshold_method_statistics",
    "cast_gtf_to_genes",
    "cast_matrix_to_numeric",
    "filter_genes_transcript",
    "get_methods_calculate_noise_threshold",
    "get_methods_correlation_distance",
    "noisyr",
    "noisyr_counts",
    "noisyr_transcript",
    "optimise_window_length",
    "plot_expression_similarity",
    "remove_noise_from_bams",
    "remove_noise_from_matrix"
  ],
  "_help": [
    {
      "page": "calculate_expression_profile",
      "title": "Calculate the expression profile of a gene",
      "topics": [
        "calculate_expression_profile"
      ]
    },
    {
      "page": "calculate_expression_similarity_counts",
      "title": "Calcualate the expression levels and expression levels similarity matrices using the count matrix",
      "topics": [
        "calculate_expression_similarity_counts"
      ]
    },
    {
      "page": "calculate_expression_similarity_transcript",
      "title": "Calcualte the distance matrices using the BAM files",
      "topics": [
        "calculate_expression_similarity_transcript"
      ]
    },
    {
      "page": "calculate_first_minimum_density",
      "title": "Function to find the first local minimum of the density of a vector",
      "topics": [
        "calculate_first_minimum_density"
      ]
    },
    {
      "page": "calculate_noise_threshold",
      "title": "Function to calculate the noise threshold for a given expression matrix and parameters",
      "topics": [
        "calculate_noise_threshold"
      ]
    },
    {
      "page": "calculate_noise_threshold_method_statistics",
      "title": "Function to tabulate statistics for different methods of calculating the noise threshold",
      "topics": [
        "calculate_noise_threshold_method_statistics"
      ]
    },
    {
      "page": "cast_gtf_to_genes",
      "title": "Function to extract exon names and positions from a gtf file",
      "topics": [
        "cast_gtf_to_genes"
      ]
    },
    {
      "page": "cast_matrix_to_numeric",
      "title": "Cast a matrix of any type to numeric",
      "topics": [
        "cast_matrix_to_numeric"
      ]
    },
    {
      "page": "filter_genes_transcript",
      "title": "Function to filter the gene table for the transcript approach",
      "topics": [
        "filter_genes_transcript"
      ]
    },
    {
      "page": "get_methods_calculate_noise_threshold",
      "title": "Show the methods for calculating a noise threshold",
      "topics": [
        "get_methods_calculate_noise_threshold"
      ]
    },
    {
      "page": "get_methods_correlation_distance",
      "title": "Show the methods for calculating correlation or distance",
      "topics": [
        "get_methods_correlation_distance"
      ]
    },
    {
      "page": "noisyr",
      "title": "Run the noisyR pipeline",
      "topics": [
        "noisyr"
      ]
    },
    {
      "page": "noisyr_counts",
      "title": "Run the noisyR pipeline for the count matrix approach",
      "topics": [
        "noisyr_counts"
      ]
    },
    {
      "page": "noisyr_transcript",
      "title": "Run the noisyR pipeline for the transcript approach",
      "topics": [
        "noisyr_transcript"
      ]
    },
    {
      "page": "optimise_window_length",
      "title": "Optimise the elements per window for the count matrix approach",
      "topics": [
        "optimise_window_length"
      ]
    },
    {
      "page": "plot_expression_similarity",
      "title": "Plot the similarity against expression levels",
      "topics": [
        "plot_expression_similarity"
      ]
    },
    {
      "page": "remove_noise_from_bams",
      "title": "Function to remove the noisy reads from the BAM files",
      "topics": [
        "remove_noise_from_bams"
      ]
    },
    {
      "page": "remove_noise_from_matrix",
      "title": "Function to remove the noisy reads from the expression matrix",
      "topics": [
        "remove_noise_from_matrix"
      ]
    }
  ],
  "_readme": "https://github.com/core-bioinformatics/noisyr/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "doParallel",
    "dplyr",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lifecycle",
    "magrittr",
    "philentropy",
    "pillar",
    "pkgconfig",
    "poorman",
    "preprocessCore",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppParallel",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "vignette_noisyr_counts.Rmd",
      "filename": "vignette_noisyr_counts.html",
      "title": "noisyR count matrix approach workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Preprocessing",
        "Running noisyR",
        "Pipeline breakdown",
        "Similarity calculation",
        "Noise quantification",
        "Noise removal",
        "Downstream analysis"
      ],
      "created": "2021-03-22 14:47:35",
      "modified": "2021-06-02 15:13:19",
      "commits": 9
    }
  ],
  "_score": 4.698970004336019,
  "_indexed": true,
  "_nocasepkg": "noisyr",
  "_universes": [
    "core-bioinformatics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-13T08:47:41.000Z",
      "distro": "noble",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "d37be4b25700dc7b87554d53bbab0f042d9054473af529f89e9d89f062ded536",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:59.000Z",
      "distro": "noble",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "c2deae4f48d060d5910cd6e2b00bab803be1e842a76cc9bdaaced678600c6291",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:28.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "803dc36f67fa1d84af6718426c3f615d2af61b64f36e887f7331effdc711be64",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:16.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "9ba9592656263d97f757c36d7878dcdced73252d4e61759126959239885e1691",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:12.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "803b5e540493c908a3377eaf3f6ca3d0bfa046352819a08f5c160bbff83ee696",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:38.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "788038ce6bc55ad4bae934ea2e63cd528616a194eb422796703e82866c71c627",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-13T08:46:18.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "967e45ccc3798db7e8ffb7da76132d6bc33e8a8b9c5f7195e9c20689e56e6be7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-22T09:51:13.000Z",
      "commit": "0c4b3b1f13a7fd88cfda969b7191647faadf6590",
      "fileid": "41b4eeb61fa2a10bed70691e427db8b63cb1bc1d174249fa5aca7fe609a32d7e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/25788170652"
    }
  ]
}