{
  "_id": "6a103b41acfb0bcc41c9b6bc",
  "Package": "UCSCXenaShiny",
  "Title": "Interactive Analysis of UCSC Xena Data",
  "Version": "2.2.1.9000",
  "Authors@R": "c(\nperson(\"Shixiang\", \"Wang\", , \"w_shixiang@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9855-7357\")),\nperson(\"Shensuo\", \"Li\", , \"lishensuo@163.com\", role = \"aut\"),\nperson(\"Yi\", \"Xiong\", , \"neuroxiong@openbiox.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4370-9824\")),\nperson(\"Longfei\", \"Zhao\", , \"longfei8533@126.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6277-0137\")),\nperson(\"Kai\", \"Gu\", , \"gukai1212@163.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0177-0774\")),\nperson(\"Yin\", \"Li\", , \"yinli18@fudan.edu.cn\", role = \"aut\"),\nperson(\"Fei\", \"Zhao\", , \"zhaofei415@mails.ucas.edu.cn\", role = \"aut\")\n)",
  "Maintainer": "Shixiang Wang <w_shixiang@163.com>",
  "Description": "Provides functions and a Shiny application for\ndownloading, analyzing and visualizing datasets from UCSC Xena\n(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted\npublic databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and\nothers.",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/openbiox/UCSCXenaShiny,\nhttps://openbiox.github.io/UCSCXenaShiny/",
  "BugReports": "https://github.com/openbiox/UCSCXenaShiny/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "NeedsCompilation": "no",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://openbiox.r-universe.dev",
  "Date/Publication": "2026-05-11 15:29:15 UTC",
  "RemoteUrl": "https://github.com/openbiox/ucscxenashiny",
  "RemoteRef": "HEAD",
  "RemoteSha": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
  "Packaged": {
    "Date": "2026-05-11 16:38:49 UTC",
    "User": "root"
  },
  "Author": "Shixiang Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9855-7357>),\nShensuo Li [aut],\nYi Xiong [aut] (ORCID: <https://orcid.org/0000-0002-4370-9824>),\nLongfei Zhao [aut] (ORCID: <https://orcid.org/0000-0002-6277-0137>),\nKai Gu [aut] (ORCID: <https://orcid.org/0000-0002-0177-0774>),\nYin Li [aut],\nFei Zhao [aut]",
  "MD5sum": "9dbbb96f4e541acb9881c0d4cea32964",
  "_user": "openbiox",
  "_type": "src",
  "_file": "UCSCXenaShiny_2.2.1.9000.tar.gz",
  "_fileid": "6ffe0722e2048bd490bb61eaf12033fc3e764775272277332d9b41460159404d",
  "_filesize": 3608059,
  "_sha256": "6ffe0722e2048bd490bb61eaf12033fc3e764775272277332d9b41460159404d",
  "_created": "2026-05-11T16:38:49.000Z",
  "_published": "2026-05-22T11:17:21.319Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77368748206,
      "time": 221,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6924365315"
    },
    {
      "job": 77368747963,
      "time": 218,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6924366367"
    },
    {
      "job": 77368748344,
      "time": 128,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6924329314"
    },
    {
      "job": 77368747782,
      "time": 176,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6924347926"
    },
    {
      "job": 77368747285,
      "time": 287,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6924280967"
    },
    {
      "job": 77368747311,
      "time": 161,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7159201735"
    },
    {
      "job": 77368747905,
      "time": 144,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6924337761"
    },
    {
      "job": 77368748194,
      "time": 184,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6924351898"
    },
    {
      "job": 77368748327,
      "time": 140,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6924334320"
    }
  ],
  "_buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/openbiox/ucscxenashiny",
  "_commit": {
    "id": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
    "author": "Shixiang Wang (王诗翔) <wangshx@csu.edu.cn>",
    "committer": "Shixiang Wang (王诗翔) <wangshx@csu.edu.cn>",
    "message": "Update pan-cancer and PCAWG documentation\n\nAdd a 'norm' parameter to the roxygen docs and man page for pan-cancer value functions, correct the description for get_pancan_methylation_value (methylation, not gene expression), and update the get_pcawg_APOBEC_mutagenesis_value description to indicate APOBEC mutagenesis. Changes made in R/get_pancan_value.R, R/get_pcawg_value.R and man/get_pancan_value.Rd to keep documentation consistent.\n",
    "time": 1778513355
  },
  "_maintainer": {
    "name": "Shixiang Wang",
    "email": "w_shixiang@163.com",
    "login": "shixiangwang",
    "orcid": "0000-0001-9855-7357",
    "twitter": "@WangShxiang",
    "uuid": 25057508
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 0.8.3",
      "role": "Imports"
    },
    {
      "package": "ezcox",
      "role": "Imports"
    },
    {
      "package": "forcats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.2.0",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "version": ">= 0.2",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "version": ">= 1.5",
      "role": "Imports"
    },
    {
      "package": "ppcor",
      "role": "Imports"
    },
    {
      "package": "psych",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "version": ">= 1.3.2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 2.1.3",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "UCSCXenaTools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "covr",
      "version": ">= 3.2.1",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "version": ">= 0.5",
      "role": "Suggests"
    },
    {
      "package": "funkyheatmap",
      "role": "Suggests"
    },
    {
      "package": "furrr",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "role": "Suggests"
    },
    {
      "package": "ggstatsplot",
      "role": "Suggests"
    },
    {
      "package": "glue",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "pacman",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "plyr",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "version": ">= 1.1.2",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "Rtsne",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "survival",
      "role": "Suggests"
    },
    {
      "package": "survminer",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.0.1",
      "role": "Suggests"
    },
    {
      "package": "umap",
      "role": "Suggests"
    }
  ],
  "_owner": "openbiox",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-31",
      "n": 2
    },
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 1
    },
    {
      "week": "2025-37",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 5
    },
    {
      "week": "2026-19",
      "n": 8
    },
    {
      "week": "2026-20",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v2.2.0",
      "date": "2025-08-01"
    },
    {
      "name": "v2.2.1",
      "date": "2026-05-05"
    }
  ],
  "_topics": [
    "cancer-dataset",
    "shiny-apps",
    "ucsc-xena"
  ],
  "_stars": 104,
  "_contributors": [
    {
      "user": "shixiangwang",
      "count": 444,
      "uuid": 25057508
    },
    {
      "user": "byronxy",
      "count": 193,
      "uuid": 28949856
    },
    {
      "user": "lishensuo",
      "count": 111,
      "uuid": 80585985
    },
    {
      "user": "longfei8533",
      "count": 32,
      "uuid": 37660840
    },
    {
      "user": "kaigu1990",
      "count": 8,
      "uuid": 22772592
    },
    {
      "user": "mugpeng",
      "count": 3,
      "uuid": 52995448
    },
    {
      "user": "yinlisssss",
      "count": 3,
      "uuid": 38618580
    },
    {
      "user": "copilot",
      "count": 2,
      "uuid": 198982749
    },
    {
      "user": "fei0810",
      "count": 1,
      "uuid": 17489298
    },
    {
      "user": "likelet",
      "count": 1,
      "uuid": 3021506
    },
    {
      "user": "qins",
      "count": 1,
      "uuid": 3041080
    }
  ],
  "_userbio": {
    "uuid": 48252911,
    "type": "organization",
    "name": "openbiox",
    "description": "A community-driven bioinformatics innovation collaboration group."
  },
  "_downloads": {
    "count": 566,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/UCSCXenaShiny"
  },
  "_devurl": "https://github.com/openbiox/ucscxenashiny",
  "_pkgdown": "https://openbiox.github.io/UCSCXenaShiny/",
  "_searchresults": 87,
  "_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/UCSCXenaShiny.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/openbiox/ucscxenashiny",
  "_realowner": "openbiox",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2019-05-09"
    },
    {
      "version": "0.1.1",
      "date": "2019-05-19"
    },
    {
      "version": "0.2.0",
      "date": "2019-07-10"
    },
    {
      "version": "0.3.0",
      "date": "2019-08-23"
    },
    {
      "version": "0.4.0",
      "date": "2019-11-02"
    },
    {
      "version": "0.5.0",
      "date": "2020-06-03"
    },
    {
      "version": "1.0.0",
      "date": "2021-05-16"
    },
    {
      "version": "1.0.1",
      "date": "2021-06-23"
    },
    {
      "version": "1.1.0",
      "date": "2021-07-16"
    },
    {
      "version": "1.1.1",
      "date": "2021-07-30"
    },
    {
      "version": "1.1.2",
      "date": "2021-11-17"
    },
    {
      "version": "1.1.3",
      "date": "2021-11-29"
    },
    {
      "version": "1.1.4",
      "date": "2021-12-13"
    },
    {
      "version": "1.1.5",
      "date": "2022-01-15"
    },
    {
      "version": "1.1.7",
      "date": "2022-04-13"
    },
    {
      "version": "1.1.8",
      "date": "2022-06-07"
    },
    {
      "version": "1.1.9",
      "date": "2022-12-12"
    },
    {
      "version": "1.1.10",
      "date": "2023-02-28"
    },
    {
      "version": "2.0.0",
      "date": "2024-03-14"
    },
    {
      "version": "2.1.0",
      "date": "2024-05-15"
    },
    {
      "version": "2.2.0",
      "date": "2025-08-01"
    },
    {
      "version": "2.2.1",
      "date": "2026-05-05"
    }
  ],
  "_exports": [
    ".opt_pancan",
    "%>%",
    "analyze_gene_drug_response_asso",
    "analyze_gene_drug_response_diff",
    "app_run",
    "app_run2",
    "available_hosts",
    "ezcor",
    "ezcor_batch",
    "ezcor_partial_cor",
    "get_ccle_cn_value",
    "get_ccle_gene_value",
    "get_ccle_mutation_status",
    "get_ccle_protein_value",
    "get_nonomics_value",
    "get_pancan_cn_value",
    "get_pancan_gene_value",
    "get_pancan_methylation_value",
    "get_pancan_miRNA_value",
    "get_pancan_mutation_status",
    "get_pancan_protein_value",
    "get_pancan_transcript_value",
    "get_pancan_value",
    "get_pcawg_APOBEC_mutagenesis_value",
    "get_pcawg_cn_value",
    "get_pcawg_fusion_value",
    "get_pcawg_gene_value",
    "get_pcawg_miRNA_value",
    "get_pcawg_mutation_status",
    "get_pcawg_promoter_value",
    "keep_cat_cols",
    "load_data",
    "mol_quick_analysis",
    "query_molecule_value",
    "query_pancan_value",
    "query_tcga_group",
    "query_toil_value_df",
    "tcga_surv_get",
    "tcga_surv_plot",
    "vis_ccle_gene_cor",
    "vis_ccle_gene_cross_omics",
    "vis_ccle_tpm",
    "vis_dim_dist",
    "vis_gene_cor",
    "vis_gene_cor_cancer",
    "vis_gene_cross_omics",
    "vis_gene_drug_response_asso",
    "vis_gene_drug_response_diff",
    "vis_gene_immune_cor",
    "vis_gene_msi_cor",
    "vis_gene_pw_cor",
    "vis_gene_stemness_cor",
    "vis_gene_TIL_cor",
    "vis_gene_tmb_cor",
    "vis_identifier_cor",
    "vis_identifier_dim_dist",
    "vis_identifier_grp_comparison",
    "vis_identifier_grp_surv",
    "vis_identifier_multi_cor",
    "vis_pancan_anatomy",
    "vis_pcawg_dist",
    "vis_pcawg_gene_cor",
    "vis_pcawg_gene_cross_omics",
    "vis_pcawg_pathway_cross_omics",
    "vis_pcawg_unicox_tree",
    "vis_toil_Mut",
    "vis_toil_Mut_cancer",
    "vis_toil_TvsN",
    "vis_toil_TvsN_cancer",
    "vis_unicox_tree"
  ],
  "_datasets": [
    {
      "name": "ccle_absolute",
      "title": "ABSOLUTE Result of CCLE Database",
      "object": "ccle_absolute",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Cell Line",
        "Lineage",
        "Purity",
        "Ploidy",
        "Genome Doublings"
      ],
      "rows": 998,
      "table": true,
      "tojson": true
    },
    {
      "name": "ccle_info",
      "title": "Phenotype Info of CCLE Database",
      "object": "ccle_info",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CCLE_name",
        "Cell_line_primary_name",
        "Cell_line_aliases",
        "Gender",
        "Site_Primary",
        "Histology",
        "Hist_Subtype1",
        "Notes",
        "Source",
        "Expression_arrays",
        "SNP_arrays",
        "Oncomap",
        "Hybrid_Capture_Sequencing",
        "Type"
      ],
      "rows": 1046,
      "table": true,
      "tojson": true
    },
    {
      "name": "ccle_info_fine",
      "title": "Cleaned Phenotype Info of CCLE Database for grouping",
      "object": "ccle_info_fine",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Site_Primary",
        "Gender",
        "Histology",
        "Type"
      ],
      "rows": 1046,
      "table": true,
      "tojson": true
    },
    {
      "name": "pcawg_info",
      "title": "Phenotype Info of PCAWG Database",
      "object": "pcawg_info",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "icgc_specimen_id",
        "donor",
        "dcc_specimen_type",
        "dcc_project_code",
        "organ_system",
        "histology_abbreviation",
        "histology_tier1",
        "histology_tier2",
        "histology_tier3",
        "histology_tier4",
        "tumour_histological_code",
        "tumour_histological_type",
        "tumour_stage",
        "tumour_grade",
        "percentage_cellularity",
        "donor_sex",
        "donor_diagnosis_icd10",
        "first_therapy_type",
        "first_therapy_response",
        "donor_age_at_diagnosis",
        "tobacco_smoking_history_indicator",
        "tobacco_smoking_intensity",
        "alcohol_history",
        "alcohol_history_intensity",
        "OS",
        "OS.time",
        "type2"
      ],
      "rows": 6231,
      "table": true,
      "tojson": true
    },
    {
      "name": "pcawg_info_fine",
      "title": "Cleaned Phenotype Info of PCAWG Database for grouping",
      "object": "pcawg_info_fine",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Project",
        "Age",
        "Gender",
        "Type"
      ],
      "rows": 1523,
      "table": true,
      "tojson": true
    },
    {
      "name": "pcawg_purity",
      "title": "Purity Data of PCAWG",
      "object": "pcawg_purity",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "icgc_specimen_id",
        "purity",
        "ploidy",
        "purity_conf_mad",
        "wgd_status",
        "wgd_uncertain"
      ],
      "rows": 2778,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_clinical",
      "title": "Toil Hub: TCGA Clinical Data",
      "object": "tcga_clinical",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample",
        "patient",
        "type",
        "age_at_initial_pathologic_diagnosis",
        "gender",
        "race",
        "ajcc_pathologic_tumor_stage",
        "clinical_stage",
        "histological_type",
        "histological_grade",
        "initial_pathologic_dx_year",
        "menopause_status",
        "vital_status",
        "tumor_status",
        "cause_of_death",
        "new_tumor_event_type",
        "new_tumor_event_site",
        "new_tumor_event_site_other",
        "new_tumor_event_dx_days_to",
        "margin_status",
        "residual_tumor",
        "BatchId"
      ],
      "rows": 12653,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_clinical_fine",
      "title": "Toil Hub: Cleaned TCGA Clinical Data for grouping",
      "object": "tcga_clinical_fine",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Cancer",
        "Age",
        "Code",
        "Gender",
        "Stage_ajcc",
        "Stage_clinical",
        "Grade"
      ],
      "rows": 12591,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_genome_instability",
      "title": "TCGA: Genome Instability Data",
      "object": "tcga_genome_instability",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "purity",
        "ploidy",
        "Genome_doublings",
        "Cancer_DNA_fraction",
        "Subclonal_genome_fraction"
      ],
      "rows": 9997,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_gtex",
      "title": "Toil Hub: Merged TCGA GTEx Selected Phenotype",
      "object": "tcga_gtex",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "tissue",
        "type",
        "type2"
      ],
      "rows": 18102,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_purity",
      "title": "TCGA: Purity Data",
      "object": "tcga_purity",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample",
        "cancer_type",
        "ESTIMATE",
        "ABSOLUTE",
        "LUMP",
        "IHC",
        "CPE"
      ],
      "rows": 9364,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_subtypes",
      "title": "TCGA Subtype Data",
      "object": "tcga_subtypes",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sampleID",
        "Subtype_mRNA",
        "Subtype_DNAmeth",
        "Subtype_protein",
        "Subtype_miRNA",
        "Subtype_CNA",
        "Subtype_Integrative",
        "Subtype_other",
        "Subtype_Selected",
        "Subtype_Immune_Model_Based"
      ],
      "rows": 10469,
      "table": true,
      "tojson": true
    },
    {
      "name": "tcga_surv",
      "title": "Toil Hub: TCGA Survival Data",
      "object": "tcga_surv",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "OS",
        "OS.time",
        "DSS",
        "DSS.time",
        "DFI",
        "DFI.time",
        "PFI",
        "PFI.time"
      ],
      "rows": 10496,
      "table": true,
      "tojson": true
    },
    {
      "name": "TCGA.organ",
      "title": "TCGA: Organ Data",
      "object": "TCGA.organ",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TCGA",
        "Detail",
        "organ"
      ],
      "rows": 33,
      "table": true,
      "tojson": true
    },
    {
      "name": "toil_info",
      "title": "Toil Hub: TCGA TARGET GTEX Selected Phenotype",
      "object": "toil_info",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "detailed_category",
        "primary disease or tissue",
        "_primary_site",
        "_sample_type",
        "_gender",
        "_study"
      ],
      "rows": 19131,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-opt_pancan",
      "title": "A default setting for pan-cancer studies",
      "topics": [
        ".opt_pancan"
      ]
    },
    {
      "page": "analyze_gene_drug_response_asso",
      "title": "Analyze Association between Gene (Signature) and Drug Response with CCLE Data",
      "topics": [
        "analyze_gene_drug_response_asso"
      ]
    },
    {
      "page": "analyze_gene_drug_response_diff",
      "title": "Analyze Difference of Drug Response (IC50 Value (uM)) between Gene (Signature) High and Low Expression with CCLE Data",
      "topics": [
        "analyze_gene_drug_response_diff"
      ]
    },
    {
      "page": "app_run",
      "title": "Run UCSC Xena Shiny App",
      "topics": [
        "app_run"
      ]
    },
    {
      "page": "app_run2",
      "title": "Run UCSC Xena Shiny App with specifc content",
      "topics": [
        "app_run2"
      ]
    },
    {
      "page": "available_hosts",
      "title": "Show Available Hosts",
      "topics": [
        "available_hosts"
      ]
    },
    {
      "page": "ccle_absolute",
      "title": "ABSOLUTE Result of CCLE Database",
      "topics": [
        "ccle_absolute"
      ]
    },
    {
      "page": "ccle_info",
      "title": "Phenotype Info of CCLE Database",
      "topics": [
        "ccle_info"
      ]
    },
    {
      "page": "ccle_info_fine",
      "title": "Cleaned Phenotype Info of CCLE Database for grouping",
      "topics": [
        "ccle_info_fine"
      ]
    },
    {
      "page": "ezcor",
      "title": "Run Correlation between Two Variables and Support Group by a Variable",
      "topics": [
        "ezcor"
      ]
    },
    {
      "page": "ezcor_batch",
      "title": "Run correlation between two variables in a batch mode and support group by a variable",
      "topics": [
        "ezcor_batch"
      ]
    },
    {
      "page": "ezcor_partial_cor",
      "title": "Run partial correlation",
      "topics": [
        "ezcor_partial_cor"
      ]
    },
    {
      "page": "get_pancan_value",
      "title": "Fetch Identifier Value from Pan-cancer Dataset",
      "topics": [
        "get_ccle_cn_value",
        "get_ccle_gene_value",
        "get_ccle_mutation_status",
        "get_ccle_protein_value",
        "get_pancan_cn_value",
        "get_pancan_gene_value",
        "get_pancan_methylation_value",
        "get_pancan_miRNA_value",
        "get_pancan_mutation_status",
        "get_pancan_protein_value",
        "get_pancan_transcript_value",
        "get_pancan_value",
        "get_pcawg_APOBEC_mutagenesis_value",
        "get_pcawg_cn_value",
        "get_pcawg_fusion_value",
        "get_pcawg_gene_value",
        "get_pcawg_miRNA_value",
        "get_pcawg_mutation_status",
        "get_pcawg_promoter_value"
      ]
    },
    {
      "page": "get_nonomics_value",
      "title": "Fetch non-omics data of all samples from relevant databases",
      "topics": [
        "get_nonomics_value"
      ]
    },
    {
      "page": "keep_cat_cols",
      "title": "Keep Only Columns Used for Sample Selection",
      "topics": [
        "keep_cat_cols"
      ]
    },
    {
      "page": "load_data",
      "title": "Load Dataset Provided by This Package",
      "topics": [
        "load_data"
      ]
    },
    {
      "page": "mol_quick_analysis",
      "title": "Quick molecule analysis and report generation",
      "topics": [
        "mol_quick_analysis"
      ]
    },
    {
      "page": "pcawg_info",
      "title": "Phenotype Info of PCAWG Database",
      "topics": [
        "pcawg_info"
      ]
    },
    {
      "page": "pcawg_info_fine",
      "title": "Cleaned Phenotype Info of PCAWG Database for grouping",
      "topics": [
        "pcawg_info_fine"
      ]
    },
    {
      "page": "pcawg_purity",
      "title": "Purity Data of PCAWG",
      "topics": [
        "pcawg_purity"
      ]
    },
    {
      "page": "query_general_value",
      "title": "Download data for shiny general analysis",
      "topics": [
        "query_general_value"
      ]
    },
    {
      "page": "query_molecule_value",
      "title": "Get Molecule or Signature Data Values from Dense (Genomic) Matrix Dataset of UCSC Xena Data Hubs",
      "topics": [
        "query_molecule_value"
      ]
    },
    {
      "page": "query_pancan_value",
      "title": "Query Single Identifier or Signature Value from Pan-cancer Database",
      "topics": [
        "query_pancan_value"
      ]
    },
    {
      "page": "query_tcga_group",
      "title": "Group TPC samples by build-in or custom phenotype and support filtering or merging operations",
      "topics": [
        "query_tcga_group"
      ]
    },
    {
      "page": "query_toil_value_df",
      "title": "Obtain ToilHub Info for Single Molecule",
      "topics": [
        "query_toil_value_df"
      ]
    },
    {
      "page": "tcga_surv_analysis",
      "title": "TCGA Survival Analysis",
      "topics": [
        "tcga survival analysis",
        "tcga_surv_get",
        "tcga_surv_plot"
      ]
    },
    {
      "page": "tcga_clinical",
      "title": "Toil Hub: TCGA Clinical Data",
      "topics": [
        "tcga_clinical"
      ]
    },
    {
      "page": "tcga_clinical_fine",
      "title": "Toil Hub: Cleaned TCGA Clinical Data for grouping",
      "topics": [
        "tcga_clinical_fine"
      ]
    },
    {
      "page": "tcga_genome_instability",
      "title": "TCGA: Genome Instability Data",
      "topics": [
        "tcga_genome_instability"
      ]
    },
    {
      "page": "tcga_gtex",
      "title": "Toil Hub: Merged TCGA GTEx Selected Phenotype",
      "topics": [
        "tcga_gtex"
      ]
    },
    {
      "page": "tcga_purity",
      "title": "TCGA: Purity Data",
      "topics": [
        "tcga_purity"
      ]
    },
    {
      "page": "tcga_subtypes",
      "title": "TCGA Subtype Data",
      "topics": [
        "tcga_subtypes"
      ]
    },
    {
      "page": "tcga_surv",
      "title": "Toil Hub: TCGA Survival Data",
      "topics": [
        "tcga_surv"
      ]
    },
    {
      "page": "tcga_tmb",
      "title": "TCGA: TMB (Tumor Mutation Burden) Data",
      "topics": [
        "tcga_tmb"
      ]
    },
    {
      "page": "TCGA.organ",
      "title": "TCGA: Organ Data",
      "topics": [
        "TCGA.organ"
      ]
    },
    {
      "page": "toil_info",
      "title": "Toil Hub: TCGA TARGET GTEX Selected Phenotype",
      "topics": [
        "toil_info"
      ]
    },
    {
      "page": "vis_ccle_gene_cor",
      "title": "Visualize CCLE Gene Expression Correlation",
      "topics": [
        "vis_ccle_gene_cor"
      ]
    },
    {
      "page": "vis_ccle_gene_cross_omics",
      "title": "Visualize cross-omics of one gene in CCLE",
      "topics": [
        "vis_ccle_gene_cross_omics"
      ]
    },
    {
      "page": "vis_ccle_tpm",
      "title": "Visualize CCLE Gene Expression",
      "topics": [
        "vis_ccle_tpm"
      ]
    },
    {
      "page": "vis_dim_dist",
      "title": "Visualize the distribution difference of samples after dimensionality reduction analysis",
      "topics": [
        "vis_dim_dist"
      ]
    },
    {
      "page": "vis_gene_cor",
      "title": "Visualize Gene-Gene Correlation in TCGA",
      "topics": [
        "vis_gene_cor"
      ]
    },
    {
      "page": "vis_gene_cor_cancer",
      "title": "Visualize Gene-Gene Correlation in a TCGA Cancer Type",
      "topics": [
        "vis_gene_cor_cancer"
      ]
    },
    {
      "page": "vis_gene_cross_omics",
      "title": "Visualize cross-omics of one gene among pan-cancers",
      "topics": [
        "vis_gene_cross_omics"
      ]
    },
    {
      "page": "vis_gene_drug_response_asso",
      "title": "Visualize Gene and Drug-Target Association with CCLE Data",
      "topics": [
        "vis_gene_drug_response_asso"
      ]
    },
    {
      "page": "vis_gene_drug_response_diff",
      "title": "Visualize Gene and Drug Response Difference with CCLE Data",
      "topics": [
        "vis_gene_drug_response_diff"
      ]
    },
    {
      "page": "vis_gene_immune_cor",
      "title": "Heatmap for Correlation between Gene and Immune Signatures",
      "topics": [
        "vis_gene_immune_cor"
      ]
    },
    {
      "page": "vis_gene_msi_cor",
      "title": "Visualize Correlation between Gene and MSI (Microsatellite instability)",
      "topics": [
        "vis_gene_msi_cor"
      ]
    },
    {
      "page": "vis_gene_pw_cor",
      "title": "Visualize Correlation between Gene and Pathway signature Score",
      "topics": [
        "vis_gene_pw_cor"
      ]
    },
    {
      "page": "vis_gene_stemness_cor",
      "title": "Visualize Correlation between Gene and Tumor Stemness",
      "topics": [
        "vis_gene_stemness_cor"
      ]
    },
    {
      "page": "vis_gene_TIL_cor",
      "title": "Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)",
      "topics": [
        "vis_gene_TIL_cor"
      ]
    },
    {
      "page": "vis_gene_tmb_cor",
      "title": "Visualize Correlation between Gene and TMB (Tumor Mutation Burden)",
      "topics": [
        "vis_gene_tmb_cor"
      ]
    },
    {
      "page": "vis_identifier_cor",
      "title": "Visualize Identifier-Identifier Correlation",
      "topics": [
        "vis_identifier_cor"
      ]
    },
    {
      "page": "vis_identifier_dim_dist",
      "title": "Visualize the distribution difference of samples after Molecule Identifier dimensionality reduction analysis",
      "topics": [
        "vis_identifier_dim_dist"
      ]
    },
    {
      "page": "vis_identifier_grp_comparison",
      "title": "Visualize Comparison of an Molecule Identifier between Groups",
      "topics": [
        "vis_identifier_grp_comparison"
      ]
    },
    {
      "page": "vis_identifier_grp_surv",
      "title": "Visualize Identifier Group Survival Difference",
      "topics": [
        "vis_identifier_grp_surv"
      ]
    },
    {
      "page": "vis_identifier_multi_cor",
      "title": "Visualize Correlation for Multiple Identifiers",
      "topics": [
        "vis_identifier_multi_cor"
      ]
    },
    {
      "page": "vis_pancan_anatomy",
      "title": "Visualize Single Gene Expression in Anatomy Location",
      "topics": [
        "vis_pancan_anatomy"
      ]
    },
    {
      "page": "vis_pcawg_dist",
      "title": "Visualize molecular profile in PCAWG",
      "topics": [
        "vis_pcawg_dist"
      ]
    },
    {
      "page": "vis_pcawg_gene_cor",
      "title": "Visualize Gene-Gene Correlation in TCGA",
      "topics": [
        "vis_pcawg_gene_cor"
      ]
    },
    {
      "page": "vis_pcawg_gene_cross_omics",
      "title": "Visualize cross-omics of one gene in PCAWG",
      "topics": [
        "vis_pcawg_gene_cross_omics"
      ]
    },
    {
      "page": "vis_pcawg_pathway_cross_omics",
      "title": "Visualize cross-omics of one pathway in PCAWG",
      "topics": [
        "vis_pcawg_pathway_cross_omics"
      ]
    },
    {
      "page": "vis_pcawg_unicox_tree",
      "title": "Visualize Single Gene Univariable Cox Result in PCAWG",
      "topics": [
        "vis_pcawg_unicox_tree"
      ]
    },
    {
      "page": "vis_toil_Mut",
      "title": "Visualize molecular profile difference between mutation and wild status of queried gene",
      "topics": [
        "vis_toil_Mut"
      ]
    },
    {
      "page": "vis_toil_Mut_cancer",
      "title": "Visualize molecular profile difference between mutation and wild status of queried gene in Single Cancer Type",
      "topics": [
        "vis_toil_Mut_cancer"
      ]
    },
    {
      "page": "vis_toil_TvsN",
      "title": "Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA & GTEx))",
      "topics": [
        "vis_toil_TvsN"
      ]
    },
    {
      "page": "vis_toil_TvsN_cancer",
      "title": "Visualize Gene TPM in Single Cancer Type (Tumor (TCGA) vs Normal (TCGA & GTEx))",
      "topics": [
        "vis_toil_TvsN_cancer"
      ]
    },
    {
      "page": "vis_unicox_tree",
      "title": "Visualize Single Gene Univariable Cox Result from Toil Data Hub",
      "topics": [
        "vis_unicox_tree"
      ]
    }
  ],
  "_readme": "https://github.com/openbiox/ucscxenashiny/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "backports",
    "base64enc",
    "bit",
    "bit64",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "cli",
    "clipr",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "ezcox",
    "farver",
    "fastmap",
    "fontawesome",
    "forcats",
    "forecast",
    "forestmodel",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "GPArotation",
    "gridExtra",
    "gtable",
    "hms",
    "htmltools",
    "httpuv",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "mnormt",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "polynom",
    "ppcor",
    "prettyunits",
    "progress",
    "promises",
    "psych",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "rstatix",
    "S7",
    "sass",
    "scales",
    "shiny",
    "sourcetools",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tzdb",
    "UCSCXenaTools",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xtable",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "api.Rmd",
      "filename": "api.html",
      "title": "Examples of Accessible Functions",
      "author": "Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Tutorial Book",
        "Fetch Data",
        "Fetch Gene Expression",
        "Fetch Transcript Expression",
        "Fetch Gene CNV",
        "Fetch Gene Mutation",
        "Fetch miRNA mature strand expression",
        "Data Visualization",
        "Visualize Single Gene Expression in PANCAN Dataset",
        "Compare Gene Expression Level in Single Cancer Type",
        "Compare Gene Expression Level in Different Anatomic Regions",
        "Visualize Relationship between Gene Expression and Prognosis in the PANCAN Dataset",
        "Other Functions and Data"
      ],
      "created": "2021-03-26 10:34:59",
      "modified": "2024-07-18 09:20:33",
      "commits": 11
    }
  ],
  "_score": 8.500620636267675,
  "_indexed": true,
  "_nocasepkg": "ucscxenashiny",
  "_universes": [
    "openbiox",
    "shixiangwang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:42:10.000Z",
      "distro": "noble",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "f6bec14b12c8e7ee9148ce5339874f79e370720e2dffb4d113c0bf860f0e113d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:42:17.000Z",
      "distro": "noble",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "342428497cab855162dc834d3156bb27048409c4dd28e6bed7bd430a29618d33",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:40:54.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "273096954aec45ea91e706624c1a9eed68018c03fd76c2a5180f24cd83fc75dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:41:19.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "b00596c69a23db7c36a667210b26f65e55770d6ec766f8f61114df0fb7080b33",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:40:42.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "627e32c7382409c571774488d0a8a2ecc588c6a64b17f86a8628a05e65493e68",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:41:26.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "378247f618fc7c76b9c480535a3b5b9c8f471a8f74c6c1afbb171d599414a1a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.2.1.9000",
      "date": "2026-05-11T16:40:37.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "1df97a3af6114086784a9acec63ae8d7741338e6a10b7ed77567285a4b80a7a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.2.1.9000",
      "date": "2026-05-22T11:17:03.000Z",
      "commit": "e012e4a3e77702863dc639bfc8ee23c8e48e3231",
      "fileid": "d535558d140d0eee510302de2d68ff40772f9af384c1ab7328df6f96e1ada7a9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/openbiox/actions/runs/25683360265"
    }
  ]
}