GDCdownload             Download GDC data
GDCprepare              Prepare GDC data
GDCprepare_clinic       Parsing clinical xml files
GDCquery                Query GDC data
GDCquery_Maf            Retrieve open access maf files from GDC server
GDCquery_clinic         Get GDC clinical data
TCGAVisualize_volcano   Creates a volcano plot for DNA methylation or
                        expression
TCGAanalyze_Clustering
                        Hierarchical cluster analysis
TCGAanalyze_DEA         Differentially expression analysis (DEA) using
                        edgeR package.
TCGAanalyze_DEA_Affy    Differentially expression analysis (DEA) using
                        limma package.
TCGAanalyze_DMR         Differentially methylated regions Analysis
TCGAanalyze_EA          Enrichment analysis of a gene-set with GO
                        [BP,MF,CC] and pathways.
TCGAanalyze_EAcomplete
                        Enrichment analysis for Gene Ontology (GO)
                        [BP,MF,CC] and Pathways
TCGAanalyze_Filtering   Filtering mRNA transcripts and miRNA selecting
                        a threshold.
TCGAanalyze_LevelTab    Adding information related to DEGs genes from
                        DEA as mean values in two conditions.
TCGAanalyze_Normalization
                        normalization mRNA transcripts and miRNA using
                        EDASeq package.
TCGAanalyze_Pathview    Generate pathview graph
TCGAanalyze_Preprocessing
                        Array Array Intensity correlation (AAIC) and
                        correlation boxplot to define outlier
TCGAanalyze_SurvivalKM
                        survival analysis (SA) univariate with
                        Kaplan-Meier (KM) method.
TCGAanalyze_analyseGRN
                        Generate network
TCGAanalyze_networkInference
                        infer gene regulatory networks
TCGAanalyze_survival    Creates survival analysis
TCGAbiolinks            The aim of TCGAbiolinks is : i) facilitate the
                        TCGA open-access data retrieval, ii) prepare
                        the data using the appropriate pre-processing
                        strategies, iii) provide the means to carry out
                        different standard analyses and iv) allow the
                        user to download a specific version of the data
                        and thus to easily reproduce earlier research
                        results.  In more detail, the package provides
                        multiple methods for analysis (e.g.,
                        differential expression analysis, identifying
                        differentially methylated regions) and methods
                        for visualization (e.g., survival plots,
                        volcano plots, starburst plots) in order to
                        easily develop complete analysis pipelines.
TCGAprepare_Affy        Prepare CEL files into an AffyBatch.
TCGAprepare_elmer       Prepare the data for ELEMR package
TCGAquery_MatchedCoupledSampleTypes
                        Retrieve multiple tissue types from the same
                        patients.
TCGAquery_SampleTypes   Retrieve multiple tissue types not from the
                        same patients.
TCGAquery_subtype       Retrieve molecular subtypes for a given tumor
TCGAvisualize_BarPlot   Barplot of subtypes and clinical info in groups
                        of gene expression clustered.
TCGAvisualize_EAbarplot
                        barPlot for a complete Enrichment Analysis
TCGAvisualize_Heatmap   Heatmap with more sensible behavior using
                        heatmap.plus
TCGAvisualize_PCA       Principal components analysis (PCA) plot
TCGAvisualize_SurvivalCoxNET
                        Survival analysis with univariate Cox
                        regression package (dnet)
TCGAvisualize_meanMethylation
                        Mean methylation boxplot
TCGAvisualize_oncoprint
                        Creating a oncoprint
TCGAvisualize_starburst
                        Create starburst plot
gaiaCNVplot             Creates a plot for GAIA ouptut (all significant
                        aberrant regions.)
getAdjacencyBiogrid     Get a matrix of interactions of genes from
                        biogrid
getDataCategorySummary
                        Create a Summary table for each sample in a
                        project saying if it contains or not files for
                        a certain data category
getGDCInfo              Check GDC server status
getGDCprojects          Retrieve all GDC projects
getGistic               Download GISTIC data from firehose
getResults              Get the results table from query
isServeOK               Check GDC server status is OK
matchedMetExp           Get GDC samples with both DNA methylation
                        (HM450K) and Gene expression data from GDC
                        databse
