{
  "_id": "6a1ad20d1d7bb097a09e2c55",
  "Package": "GDCRNATools",
  "Title": "GDCRNATools: an R/Bioconductor package for integrative analysis\nof lncRNA, mRNA, and miRNA data in GDC",
  "Version": "1.33.0",
  "Author": "Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan\nMa, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia",
  "Maintainer": "Ruidong Li <rli012@ucr.edu>, Han Qu <hqu002@ucr.edu>",
  "Description": "This is an easy-to-use package for downloading,\norganizing, and integrative analyzing RNA expression data in\nGDC with an emphasis on deciphering the lncRNA-mRNA related\nceRNA regulatory network in cancer. Three databases of\nlncRNA-miRNA interactions including spongeScan, starBase, and\nmiRcode, as well as three databases of mRNA-miRNA interactions\nincluding miRTarBase, starBase, and miRcode are incorporated\ninto the package for ceRNAs network construction. limma, edgeR,\nand DESeq2 can be used to identify differentially expressed\ngenes/miRNAs. Functional enrichment analyses including GO,\nKEGG, and DO can be performed based on the clusterProfiler and\nDO packages. Both univariate CoxPH and KM survival analyses of\nmultiple genes can be implemented in the package. Besides some\nroutine visualization functions such as volcano plot, bar plot,\nand KM plot, a few simply shiny apps are developed to\nfacilitate visualization of results on a local webpage.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
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  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, GeneExpression, DifferentialExpression,\nGeneRegulation, GeneTarget, NetworkInference, Survival,\nVisualization, GeneSetEnrichment, NetworkEnrichment, Network,\nRNASeq, GO, KEGG",
  "RoxygenNote": "6.1.0",
  "Packaged": {
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:09 UTC",
  "RemoteUrl": "https://github.com/bioc/GDCRNATools",
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      "title": "This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer.",
      "topics": [
        "GDCRNATools-package",
        "GDCRNATools"
      ]
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      "title": "Output of 'gdcDEAnalysis' for downstream analysis",
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      "title": "Output of 'gdcEnrichAnalysis' for visualization",
      "topics": [
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      "title": "Bar plot of differentially expressed genes/miRNAs",
      "topics": [
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      "title": "Competing endogenous RNAs (ceRNAs) analysis",
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      "title": "Download clinical data in GDC",
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      "title": "Differential gene expression analysis",
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      "title": "Plots for enrichment analysis",
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      "topics": [
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      "page": "gdcFilterSampleType",
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      "topics": [
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      "topics": [
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      "title": "Parse metadata",
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      "topics": [
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    {
      "page": "gdcRNAMerge",
      "title": "Merge RNA/miRNAs raw counts data",
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      "title": "Shiny pathview",
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