Package: GDCRNATools
Title: GDCRNATools: an R/Bioconductor package for integrative analysis
        of lncRNA, mRNA, and miRNA data in GDC
Version: 1.33.0
Author: Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan
        Ma, 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,
        organizing, and integrative analyzing RNA expression data in
        GDC with an emphasis on deciphering the lncRNA-mRNA related
        ceRNA regulatory network in cancer. Three databases of
        lncRNA-miRNA interactions including spongeScan, starBase, and
        miRcode, as well as three databases of mRNA-miRNA interactions
        including miRTarBase, starBase, and miRcode are incorporated
        into the package for ceRNAs network construction. limma, edgeR,
        and DESeq2 can be used to identify differentially expressed
        genes/miRNAs. Functional enrichment analyses including GO,
        KEGG, and DO can be performed based on the clusterProfiler and
        DO packages. Both univariate CoxPH and KM survival analyses of
        multiple genes can be implemented in the package. Besides some
        routine visualization functions such as volcano plot, bar plot,
        and KM plot, a few simply shiny apps are developed to
        facilitate visualization of results on a local webpage.
Depends: R (>= 3.5.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,
        clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,
        survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,
        BiocParallel
Suggests: knitr, testthat, prettydoc, rmarkdown
VignetteBuilder: knitr
biocViews: ImmunoOncology, GeneExpression, DifferentialExpression,
        GeneRegulation, GeneTarget, NetworkInference, Survival,
        Visualization, GeneSetEnrichment, NetworkEnrichment, Network,
        RNASeq, GO, KEGG
RoxygenNote: 6.1.0
Packaged: 2026-07-03 18:45:57 UTC; root
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:47:09 UTC
RemoteUrl: https://github.com/bioc/GDCRNATools
RemoteRef: HEAD
RemoteSha: abb49bff0d8e8e39f3e98056b7aa17a4efb26158
NeedsCompilation: no