GDCdownload             Download GDC data
GDCprepare              Prepare GDC data
GDCprepare_clinic       Parsing clinical xml files
GDCquery                Query GDC data
GDCquery_ATAC_seq       Retrieve open access ATAC-seq files from GDC
                        server
GDCquery_clinic         Get GDC clinical data
PanCancerAtlas_subtypes
                        Retrieve table with TCGA molecular subtypes
TCGAVisualize_volcano   Creates a volcano plot for DNA methylation or
                        expression
TCGA_MolecularSubtype   Retrieve molecular subtypes for given TCGA
                        barcodes
TCGAanalyze_Clustering
                        Hierarchical cluster analysis
TCGAanalyze_DEA         Differential expression analysis (DEA) using
                        edgeR or limma package.
TCGAanalyze_DEA_Affy    Differentially expression analysis (DEA) using
                        limma package.
TCGAanalyze_DMC         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_Stemness    Generate Stemness Score based on RNASeq (mRNAsi
                        stemness index) Malta et al., Cell, 2018
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
TCGAbatch_Correction    Batch correction using ComBat and Voom
                        transformation using limma package.
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.
TCGAquery_MatchedCoupledSampleTypes
                        Retrieve multiple tissue types from the same
                        patients.
TCGAquery_SampleTypes   Retrieve multiple tissue types not from the
                        same patients.
TCGAquery_recount2      Query gene counts of TCGA and GTEx data from
                        the Recount2 project
TCGAquery_subtype       Retrieve molecular subtypes for a given tumor
TCGAtumor_purity        Filters TCGA barcodes according to purity
                        parameters
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
TabSubtypesCol_merged   TCGA samples with their Pam50 subtypes
Tumor.purity            TCGA samples with their Tumor Purity measures
UseRaw_afterFilter      Use raw count from the DataPrep object which
                        genes are removed by normalization and
                        filtering steps.
colDataPrepare          Create samples information matrix for GDC
                        samples
dmc.non.parametric      Perform non-parametrix wilcoxon test
gaiaCNVplot             Creates a plot for GAIA output (all significant
                        aberrant regions.)
get.GRCh.bioMart        Get hg19 gene annotation or hg38 (gencode v36)
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
getLinkedOmicsData      Retrieve linkedOmics data
getMC3MAF               Retrieve open access mc3 MAF file from GDC
                        server
getManifest             Get a Manifest from GDCquery output that can be
                        used with GDC-client
getNbCases              Get Number of cases in GDC for a project
getNbFiles              Get Number of files in GDC for a project
getProjectSummary       Get Project Summary from GDC
getResults              Get the results table from query
getSampleFilesSummary   Retrieve summary of files per sample in a
                        project
getTSS                  getTSS to fetch GENCODE gene annotation
                        (transcripts level) from Bioconductor package
                        biomaRt If upstream and downstream are
                        specified in TSS list, promoter regions of
                        GENCODE gene will be generated.
get_IDs                 Extract information from TCGA barcodes.
gliomaClassifier        Gliomar classifier
isServeOK               Check GDC server status is OK
matchedMetExp           Get GDC samples with both DNA methylation
                        (HM450K) and Gene expression data from GDC
                        databse
splitAPICall            internal function to break a huge API call into
                        smaller ones so it repects the max character
                        limit of a string
