GDCRNATools: an R/Bioconductor package for integrative analysis
of lncRNA, mRNA, and miRNA data in GDC
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Documentation for package ‘GDCRNATools’ version 1.29.0
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 |