Package: GDCRNATools
Title: GDCRNATools: an R/Bioconductor package for integrative analysis
        of lncRNA, mRNA, and miRNA data in GDC
Version: 1.28.0
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: 2025-04-16 00:50:58 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/GDCRNATools
git_branch: RELEASE_3_21
git_last_commit: dd67354
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Built: R 4.5.0; ; 2025-04-16 14:30:01 UTC; windows
