Man pages for Jialab-UCR/GDCRNATools
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

DEGAllOutput of 'gdcDEAnalysis' for downstream analysis
enrichOutputOutput of 'gdcEnrichAnalysis' for visualization
gdcBarPlotBar plot of differentially expressed genes/miRNAs
gdcCEAnalysisCompeting endogenous RNAs (ceRNAs) analysis
gdcClinicalDownloadDownload clinical data in GDC
gdcClinicalMergeMerge clinical data
gdcCorPlotCorrelation plot of two genes/miRNAs
gdcDEAnalysisDifferential gene expression analysis
gdcDEReportReport differentially expressed genes/miRNAs
gdcEnrichAnalysisFunctional enrichment analysis
gdcEnrichPlotPlots for enrichment analysis
gdcExportNetworkExport network for Cytoscape
gdcFilterDuplicateFilter out duplicated samples
gdcFilterSampleTypeFilter out other type of samples
gdcHeatmapHeatmap of differentially expressed genes/miRNAs
gdcKMPlotKaplan Meier plot
gdcMatchSamplesMatch samples in metadata and expression matrix
gdcParseMetadataParse metadata
gdcRNADownloadDownload RNA data in GDC
gdcRNAMergeMerge RNA/miRNAs raw counts data
GDCRNATools-packageThis is an easy-to-use package for downloading, organizing,...
gdcSurvivalAnalysisUnivariate survival analysis of multiple genes
gdcVolcanoPlotVolcano plot of differentially expressed genes/miRNAs
gdcVoomNormalizationTMM normalization and voom transformation
lncTargetmiRNA-lncRNA interactions
mirCountsmiRNA counts data of TCGA-CHOL
pcTargetmiRNA-mRNA interactions
rnaCountsRNAseq counts data of TCGA-CHOL
shinyCorPlotShiny correlation plot
shinyKMPlotShiny Kaplan Meier (KM) plot
shinyPathviewShiny pathview
Jialab-UCR/GDCRNATools documentation built on May 12, 2019, 8:38 a.m.