{
  "_id": "6aca1fe4fe5cc25786e84f5b",
  "Package": "easierData",
  "Title": "easier internal data and exemplary dataset from\nIMvigor210CoreBiologies package",
  "Version": "1.18.0",
  "Authors@R": "c(\nperson(\ngiven = \"Oscar\", family = \"Lapuente-Santana\", role = c(\"aut\", \"cre\"),\nemail = \"o.lapuente.santana@tue.nl\", comment = c(ORCID = \"0000-0003-1995-8393\")\n),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = \"aut\",\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n),\nperson(\ngiven = \"Arsenij\", family = \"Ustjanzew\", role = \"aut\",\nemail = \"arsenij.ustjanzew@uni-mainz.de\", comment = c(ORCID = \"0000-0002-1014-4521\")\n),\nperson(\ngiven = \"Francesca\", family = \"Finotello\", role = \"aut\",\nemail = \"francesca.finotello@i-med.ac.at\", comment = c(ORCID = \"0000-0003-0712-4658\")\n),\nperson(\ngiven = \"Federica\", family = \"Eduati\", role = \"aut\",\nemail = \"f.eduati@tue.nl\", comment = c(ORCID = \"0000-0002-7822-3867\")\n)\n)",
  "Description": "Access to internal data required for the functional\nperformance of easier package and exemplary bladder cancer\ndataset with both processed RNA-seq data and information on\nresponse to ICB therapy generated by Mariathasan et al. \"TGF-B\nattenuates tumour response to PD-L1 blockade by contributing to\nexclusion of T cells\", published in Nature, 2018\n[doi:10.1038/nature25501](https://doi.org/10.1038/nature25501).\nThe data is made available via\n[`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/)\npackage under the CC-BY license.",
  "License": "MIT + file LICENSE",
  "biocViews": "RNASeqData, ExperimentHub, ReproducibleResearch,\nImmunoOncologyData, CancerData, ExperimentData",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.2",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:35:55 UTC",
  "RemoteUrl": "https://github.com/bioc/easierData",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "22db2cd64818ac87d23b95fde433e6db8793ac55",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 11:15:45 UTC",
    "User": "root"
  },
  "Author": "Oscar Lapuente-Santana [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1995-8393>),\nFederico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>),\nArsenij Ustjanzew [aut] (ORCID:\n<https://orcid.org/0000-0002-1014-4521>),\nFrancesca Finotello [aut] (ORCID:\n<https://orcid.org/0000-0003-0712-4658>),\nFederica Eduati [aut] (ORCID: <https://orcid.org/0000-0002-7822-3867>)",
  "Maintainer": "Oscar Lapuente-Santana <o.lapuente.santana@tue.nl>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "easierData_1.18.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/da5a070b42185f4bbd622504a708af9f696bce3d6476fd756f60afee1d60886d",
  "_filesize": 149388,
  "_sha256": "da5a070b42185f4bbd622504a708af9f696bce3d6476fd756f60afee1d60886d",
  "_expires": "2027-01-18T11:22:10.000Z",
  "_created": "2026-10-10T11:15:45.000Z",
  "_published": "2026-10-10T11:22:12.297Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047569010",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_upstream": "https://github.com/bioc/easierData",
  "_commit": {
    "id": "22db2cd64818ac87d23b95fde433e6db8793ac55",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379755
  },
  "_maintainer": {
    "name": "Oscar Lapuente-Santana",
    "email": "o.lapuente.santana@tue.nl",
    "login": "olapuentesantana",
    "twitter": "@LapuenteSantana",
    "description": "",
    "uuid": 42207933,
    "orcid": "0000-0003-1995-8393"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114200822021,
      "time": 159,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11668287459"
    },
    {
      "job": 114200822014,
      "time": 328,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11667883092"
    },
    {
      "job": 114200822010,
      "time": 308,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11668272815"
    },
    {
      "job": 114200134059,
      "time": 240,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668890663"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "ExperimentHub",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24",
      "repository": "data/experiment"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23",
      "repository": "data/experiment"
    }
  ],
  "_topics": [
    "rnaseqdata",
    "experimenthub",
    "reproducibleresearch",
    "immunooncologydata",
    "cancerdata",
    "experimentdata",
    "datapkg"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 10,
  "_datapkg": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/easierData.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "get_cor_scores_genes",
    "get_group_lrpairs",
    "get_HGNC_annotation",
    "get_intercell_networks",
    "get_lr_frequency_TCGA",
    "get_Mariathasan2018_PDL1_treatment",
    "get_opt_models",
    "get_opt_xtrain_stats",
    "get_scores_signature_genes",
    "get_TCGA_mean_pancancer",
    "get_TCGA_sd_pancancer",
    "list_easierData"
  ],
  "_help": [
    {
      "page": "easierData-pkg",
      "title": "easierData: easier data package",
      "topics": [
        "easierData-pkg"
      ]
    },
    {
      "page": "get_cor_scores_genes",
      "title": "Get the list of genes used to define correlated scores of immune response",
      "topics": [
        "get_cor_scores_genes"
      ]
    },
    {
      "page": "get_group_lrpairs",
      "title": "Get the groups of ligand-receptor pairs",
      "topics": [
        "get_group_lrpairs"
      ]
    },
    {
      "page": "get_HGNC_annotation",
      "title": "Get the gene symbols approved annotations",
      "topics": [
        "get_HGNC_annotation"
      ]
    },
    {
      "page": "get_intercell_networks",
      "title": "Get the cancer-specific intercellular networks, including a pan-cancer network",
      "topics": [
        "get_intercell_networks"
      ]
    },
    {
      "page": "get_lr_frequency_TCGA",
      "title": "Get the frequency of each ligand-receptor pair feature across the whole TCGA database",
      "topics": [
        "get_lr_frequency_TCGA"
      ]
    },
    {
      "page": "get_Mariathasan2018_PDL1_treatment",
      "title": "Get the Mariathasan2018 PD-L1 treatment data",
      "topics": [
        "get_Mariathasan2018_PDL1_treatment"
      ]
    },
    {
      "page": "get_opt_models",
      "title": "Get the cancer-specific model feature parameters",
      "topics": [
        "get_opt_models"
      ]
    },
    {
      "page": "get_opt_xtrain_stats",
      "title": "Get training set cancer-specific features mean and standard deviation",
      "topics": [
        "get_opt_xtrain_stats"
      ]
    },
    {
      "page": "get_scores_signature_genes",
      "title": "Get the gene signatures for each score of immune response",
      "topics": [
        "get_scores_signature_genes"
      ]
    },
    {
      "page": "get_TCGA_mean_pancancer",
      "title": "Get the mean of the TPM expression of each gene across all TCGA cancer types",
      "topics": [
        "get_TCGA_mean_pancancer"
      ]
    },
    {
      "page": "get_TCGA_sd_pancancer",
      "title": "Get the standard deviation of the TPM expression of each gene across all TCGA cancer types",
      "topics": [
        "get_TCGA_sd_pancancer"
      ]
    },
    {
      "page": "list_easierData",
      "title": "List the datasets",
      "topics": [
        "list_easierData"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/easierData/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "ExperimentHub",
    "fastmap",
    "filelock",
    "generics",
    "GenomicRanges",
    "glue",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "easierData.Rmd",
      "filename": "easierData.html",
      "title": "easier Data",
      "author": "Oscar Lapuente-Santana, Federico Marini, Arsenij Ustjanzew, Francesca Finotello, Federica Eduati",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Intro to easierData",
        "Load easier Data",
        "Session info",
        "References"
      ],
      "created": "2021-06-29 15:08:52",
      "modified": "2021-10-15 11:26:20",
      "commits": 14
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "easierdata",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/easierData",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-10T11:19:02.000Z",
      "distro": "resolute",
      "commit": "22db2cd64818ac87d23b95fde433e6db8793ac55",
      "fileid": "https://r2.ropensci.org/1049970aacfb6e8b32b653790c2e7bcdf5bcf23f5df49fea4fa9ae58871a903b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047569010"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-10T11:18:58.000Z",
      "distro": "resolute",
      "commit": "22db2cd64818ac87d23b95fde433e6db8793ac55",
      "fileid": "https://r2.ropensci.org/22314d5a870bb7704db5b164bfa2963920e8292c0287358055750a2541916a67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047569010"
    }
  ]
}