# GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

## Documentation for package ‘GDCRNATools’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GDCRNATools-package | 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.
DEGAll | Output of 'gdcDEAnalysis' for downstream analysis
enrichOutput | Output of 'gdcEnrichAnalysis' for visualization
gdcBarPlot | Bar plot of differentially expressed genes/miRNAs
gdcCEAnalysis | Competing endogenous RNAs (ceRNAs) analysis
gdcClinicalDownload | Download clinical data in GDC
gdcClinicalMerge | Merge clinical data
gdcCorPlot | Correlation plot of two genes/miRNAs
gdcDEAnalysis | Differential gene expression analysis
gdcDEReport | Report differentially expressed genes/miRNAs
gdcEnrichAnalysis | Functional enrichment analysis
gdcEnrichPlot | Plots for enrichment analysis
gdcExportNetwork | Export network for Cytoscape
gdcFilterDuplicate | Filter out duplicated samples
gdcFilterSampleType | Filter out other type of samples
gdcHeatmap | Heatmap of differentially expressed genes/miRNAs
gdcKMPlot | Kaplan Meier plot
gdcMatchSamples | Match samples in metadata and expression matrix
gdcParseMetadata | Parse metadata
gdcRNADownload | Download RNA data in GDC
gdcRNAMerge | Merge RNA/miRNAs raw counts data
GDCRNATools | 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.
gdcSurvivalAnalysis | Univariate survival analysis of multiple genes
gdcVolcanoPlot | Volcano plot of differentially expressed genes/miRNAs
gdcVoomNormalization | TMM normalization and voom transformation
lncTarget | miRNA-lncRNA interactions
mirCounts | miRNA counts data of TCGA-CHOL
pcTarget | miRNA-mRNA interactions
rnaCounts | RNAseq counts data of TCGA-CHOL
shinyCorPlot | Shiny correlation plot
shinyKMPlot | Shiny Kaplan Meier (KM) plot
shinyPathview | Shiny pathview