{
  "_id": "6ace13fba14063b82c3af55a",
  "Package": "CoSIA",
  "Type": "Package",
  "Title": "An Investigation Across Different Species and Tissues",
  "Version": "1.13.2",
  "Authors@R": "c(person(given = \"Anisha\",\nfamily = \"Haldar\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1395-9793\")),\nperson(given = c(\"Vishal\", \"H.\"),\nfamily = \"Oza\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-6990-0267\")),\nperson(given = c(\"Amanda\", \"D.\"),\nfamily = \"Clark\",\nrole = c(\"aut\"),\nemail = \"clarkaduab@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1186-3114\")),\nperson(given = c(\"Anthony\", \"B.\"),\nfamily = \"Crumley\",\nrole = c(\"cre\", \"aut\"),\nemail = \"acrumley@uab.edu\",\ncomment = c(ORCID = \"0009-0004-7347-4722\")),\nperson(given = c(\"Nathaniel\", \"S.\"),\nfamily = \"DeVoss\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-0465-2770\")),\nperson(given = c(\"Brittany\", \"N.\"),\nfamily = \"Lasseigne\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-1642-8904\")))",
  "Description": "Cross-Species Investigation and Analysis (CoSIA) is a\npackage that provides researchers with an alternative\nmethodology for comparing across species and tissues using\nnormal wild-type RNA-Seq Gene Expression data from Bgee. Using\nRNA-Seq Gene Expression data, CoSIA provides multiple\nvisualization tools to explore the transcriptome diversity and\nvariation across genes, tissues, and species. CoSIA uses the\nCoefficient of Variation and Shannon Entropy and Specificity to\ncalculate transcriptome diversity and variation. CoSIA also\nprovides additional conversion tools and utilities to provide a\nstreamlined methodology for cross-species comparison.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "biocViews": "Software, BiologicalQuestion, GeneExpression,\nMultipleComparison, ThirdPartyClient, DataImport, GUI",
  "BugReports": "https://github.com/lasseignelab/CoSIA/issues",
  "URL": "https://www.lasseigne.org/",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-30 20:31:05 UTC",
  "RemoteUrl": "https://github.com/bioc/CoSIA",
  "RemoteRef": "HEAD",
  "RemoteSha": "820de6ce0606576fee124b74bc153fc55ec2621f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-13 11:02:59 UTC",
    "User": "root"
  },
  "Author": "Anisha Haldar [aut] (ORCID: <https://orcid.org/0000-0002-1395-9793>),\nVishal H. Oza [aut] (ORCID: <https://orcid.org/0000-0001-6990-0267>),\nAmanda D. Clark [aut] (ORCID: <https://orcid.org/0000-0002-1186-3114>),\nAnthony B. Crumley [cre, aut] (ORCID:\n<https://orcid.org/0009-0004-7347-4722>),\nNathaniel S. DeVoss [aut] (ORCID:\n<https://orcid.org/0000-0003-0465-2770>),\nBrittany N. Lasseigne [aut] (ORCID:\n<https://orcid.org/0000-0002-1642-8904>)",
  "Maintainer": "Anthony B. Crumley <acrumley@uab.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "CoSIA_1.13.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/9330a934ffe9eb9090ef3f6e9d83f2d1daef9e2e250e6aca37393a3f970da673",
  "_filesize": 1053567,
  "_sha256": "9330a934ffe9eb9090ef3f6e9d83f2d1daef9e2e250e6aca37393a3f970da673",
  "_expires": "2027-01-21T11:20:24.000Z",
  "_created": "2026-10-13T11:02:59.000Z",
  "_published": "2026-10-13T11:20:26.794Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 4
  },
  "_upstream": "https://github.com/bioc/CoSIA",
  "_commit": {
    "id": "820de6ce0606576fee124b74bc153fc55ec2621f",
    "author": "Tonie Crumley <tonie.crumley@gmail.com>",
    "committer": "Tonie Crumley <tonie.crumley@gmail.com>",
    "message": "Version bump in devel\n",
    "time": 1782851465
  },
  "_maintainer": {
    "name": "Anthony B. Crumley",
    "email": "acrumley@uab.edu",
    "login": "toniecrumley",
    "description": "",
    "uuid": 148514625,
    "orcid": "0009-0004-7347-4722"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115263103819,
      "time": 261,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11807458256"
    },
    {
      "job": 115263103903,
      "time": 607,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11807124577"
    },
    {
      "job": 115263103765,
      "time": 883,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11807945741"
    },
    {
      "job": 115263103837,
      "time": 806,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11807614944"
    },
    {
      "job": 115263103845,
      "time": 985,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11808690425"
    },
    {
      "job": 115260626009,
      "time": 385,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11806942612"
    },
    {
      "job": 115263103930,
      "time": 237,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11807712153"
    },
    {
      "job": 115263103829,
      "time": 764,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11807404357"
    },
    {
      "job": 115263103932,
      "time": 658,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11806864262"
    },
    {
      "job": 115263103833,
      "time": 596,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11807134462"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "ExperimentHub",
      "version": ">= 2.7.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.7",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "version": ">= 2.0.1",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "version": ">= 1.1-2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.2.0",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "version": ">= 4.10.0",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "version": ">= 1.4.0",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.3.5",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 3.1.7",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "org.Mm.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "org.Dr.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "org.Ce.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "org.Dm.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "org.Rn.eg.db",
      "version": ">= 3.12.0",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "version": ">= 1.52.0",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "version": ">= 2.46.3",
      "role": "Imports"
    },
    {
      "package": "homologene",
      "version": ">= 1.4.68.19",
      "role": "Imports"
    },
    {
      "package": "annotationTools",
      "version": ">= 1.64.0",
      "role": "Imports"
    },
    {
      "package": "readr",
      "version": ">= 2.1.1",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "version": ">= 1.1.2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "version": ">= 4.1.2",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "version": ">= 2.22.0",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "version": ">= 1.3.1",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.42",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 2.20",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.1.6",
      "role": "Suggests"
    },
    {
      "package": "qpdf",
      "version": ">= 1.3.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 5
    },
    {
      "week": "2025-45",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 5
    },
    {
      "week": "2026-19",
      "n": 3
    },
    {
      "week": "2026-23",
      "n": 1
    },
    {
      "week": "2026-27",
      "n": 3
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.13.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.12.1",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "biologicalquestion",
    "geneexpression",
    "multiplecomparison",
    "thirdpartyclient",
    "dataimport",
    "gui"
  ],
  "_stars": 12,
  "_contributors": [
    {
      "user": "anishahaldar",
      "count": 132,
      "uuid": 77807004
    },
    {
      "user": "adc0032",
      "count": 110,
      "uuid": 18667790
    },
    {
      "user": "toniecrumley",
      "count": 25,
      "uuid": 148514625
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "vishaloza",
      "count": 2,
      "uuid": 4385311
    },
    {
      "user": "lshep",
      "count": 2,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 368,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CoSIA"
  },
  "_devurl": "https://github.com/lasseignelab/cosia",
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CoSIA.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/lasseignelab/cosia",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CoSIAn",
    "getConversion",
    "getGEx",
    "getGExMetrics",
    "getTissues",
    "plotCVGEx",
    "plotDSGEx",
    "plotSpeciesGEx",
    "plotTissueGEx",
    "viewCoSIAn"
  ],
  "_help": [
    {
      "page": "CoSIA-class",
      "title": "CoSIAn Class S4 Object",
      "topics": [
        "CoSIAn-class"
      ]
    },
    {
      "page": "CoSIA-constructor",
      "title": "Constructor for the CoSIAn Object",
      "topics": [
        "CoSIAn",
        "CoSIAn-Constructor Constructor for the CoSIAn Class"
      ]
    },
    {
      "page": "getConversion",
      "title": "getConversion Generic",
      "topics": [
        "getConversion"
      ]
    },
    {
      "page": "getConversion-CoSIAn-method",
      "title": "getConversion Method",
      "topics": [
        "getConversion,CoSIAn-method"
      ]
    },
    {
      "page": "getGEx",
      "title": "getGEx Generic",
      "topics": [
        "getGEx"
      ]
    },
    {
      "page": "getGEx-CoSIAn-method",
      "title": "getGEx Method",
      "topics": [
        "getGEx,CoSIAn-method"
      ]
    },
    {
      "page": "getGExMetrics",
      "title": "getGExMetrics Generic",
      "topics": [
        "getGExMetrics"
      ]
    },
    {
      "page": "getGExMetrics-CoSIAn-method",
      "title": "getGExMetrics Method",
      "topics": [
        "getGExMetrics,CoSIAn-method"
      ]
    },
    {
      "page": "getTissues",
      "title": "getTissues",
      "topics": [
        "getTissues"
      ]
    },
    {
      "page": "plotCVGEx",
      "title": "plotCVGEx Generic",
      "topics": [
        "plotCVGEx"
      ]
    },
    {
      "page": "plotCVGEx-CoSIAn-method",
      "title": "plotCVGEx Method",
      "topics": [
        "plotCVGEx,CoSIAn-method"
      ]
    },
    {
      "page": "plotDSGEx",
      "title": "plotDSGEx Generic",
      "topics": [
        "plotDSGEx"
      ]
    },
    {
      "page": "plotDSGEx-CoSIAn-method",
      "title": "plotDSGEx Method",
      "topics": [
        "plotDSGEx,CoSIAn-method"
      ]
    },
    {
      "page": "plotSpeciesGEx",
      "title": "plotSpeciesGEx Generic",
      "topics": [
        "plotSpeciesGEx"
      ]
    },
    {
      "page": "plotSpeciesGEx-CoSIAn-method",
      "title": "plotSpeciesGEx Method",
      "topics": [
        "plotSpeciesGEx,CoSIAn-method"
      ]
    },
    {
      "page": "plotTissueGEx",
      "title": "plotTissueGEx Generic",
      "topics": [
        "plotTissueGEx"
      ]
    },
    {
      "page": "plotTissueGEx-CoSIAn-method",
      "title": "plotTissueGEx Method",
      "topics": [
        "plotTissueGEx,CoSIAn-method"
      ]
    },
    {
      "page": "viewCoSIAn",
      "title": "viewCoSIAn Generics",
      "topics": [
        "viewCoSIAn"
      ]
    },
    {
      "page": "viewCoSIAn-CoSIAn-method",
      "title": "viewCoSIAn",
      "topics": [
        "viewCoSIAn,CoSIAn-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CoSIA/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "AnnotationHub",
    "annotationTools",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "digest",
    "dplyr",
    "evaluate",
    "ExperimentHub",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "hms",
    "homologene",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "openssl",
    "org.Ce.eg.db",
    "org.Dm.eg.db",
    "org.Dr.eg.db",
    "org.Hs.eg.db",
    "org.Mm.eg.db",
    "org.Rn.eg.db",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CoSIA_Intro.Rmd",
      "filename": "CoSIA_Intro.html",
      "title": "CoSIA, an R package for Cross Species Investigation and Analysis",
      "author": "Anisha Haldar, Vishal H. Oza, Nathaniel DeVoss, Amanda D. Clark, Brittany N. Lasseigne",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Summary",
        "Installation",
        "Generating a CoSIAn object",
        "Load CoSIA",
        "Arguments and options table",
        "Find possible tissues with getTissues",
        "Initializing a CoSIAn object",
        "Use Cases with Monogenic Kidney Disease-Associated Genes",
        "Use Case #1: Converting Gene Symbols to Ensembl IDs (getConversion)",
        "Use Case #2: Obtaining and visualizing curated non-diseased kidney and heart gene expression data for human, mouse, rat from Bgee",
        "Use Case #3: Gene expression variability across species for kidney tissue by calculating and visualizing median-based Coefficient of Variation (CV)",
        "Use Case #4: Gene expression diversity and specificity across tissues and species for monogenic kidney-disease associated genes"
      ],
      "created": "2022-12-08 19:04:47",
      "modified": "2024-10-18 20:14:47",
      "commits": 22
    }
  ],
  "_score": 6.2552725051033065,
  "_indexed": true,
  "_nocasepkg": "cosia",
  "_universes": [
    "bioc",
    "toniecrumley",
    "lasseignelab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.13.2",
      "date": "2026-10-13T11:07:37.000Z",
      "distro": "resolute",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/5b4573e22ccac7856aebe5982e2d84818c9020b640ed15ce5aa35809666877a8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.13.2",
      "date": "2026-10-13T11:08:12.000Z",
      "distro": "resolute",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/308fc69881cb09375cc1447838565f2fe42c061f847ba8780ff4d2e7c94af66a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.13.2",
      "date": "2026-10-13T11:06:10.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/0375d1d30ce971680301a3fb7f0f28dbe1b09370ecf106dcc0e3cf04498a344e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.13.2",
      "date": "2026-10-13T11:06:28.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/07594934277d0d902ef0f7dbbc8acc52a0980cd92a5ef6d8ec75c8cf6045344a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.13.2",
      "date": "2026-10-13T11:07:24.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/055f1c2a6d9427ea566e3b78f1d86d4a466f1e475ae07bd7961235fa24cbc1dc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.13.2",
      "date": "2026-10-13T11:05:30.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/73e5917d54fe69b8af068ce4a39318f36f13aa48e16a339e26b9758cc88fc7cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.13.2",
      "date": "2026-10-13T11:05:21.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/80df202d6d998b0deb4c164e577f53925d21d80ccb4bd2cfffac91ec2de2f640",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.13.2",
      "date": "2026-10-13T11:05:19.000Z",
      "commit": "820de6ce0606576fee124b74bc153fc55ec2621f",
      "fileid": "https://r2.ropensci.org/aae29c06132d60ad96072f5bf4a519fcf37109ae326550f55cf574c342b24dc9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38386806472"
    }
  ]
}