# TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

## Documentation for package ‘TCGAbiolinks’ version 2.39.0

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

## Help Pages

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.)
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
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
getManifest | Get a Manifest from GDCquery output that can be used with GDC-client
getMC3MAF | Retrieve open access mc3 MAF file from GDC server
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 primary tumors samples with both DNA methylation (HM450K) and Gene expression data
PanCancerAtlas_subtypes | Retrieve table with TCGA molecular subtypes
splitAPICall | internal function to break a huge API call into smaller ones so it repects the max character limit of a string
TabSubtypesCol_merged | TCGA samples with their Pam50 subtypes
TCGAanalyze_analyseGRN | Generate network
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_networkInference | infer gene regulatory networks
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_survival | Creates survival analysis
TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM) method.
TCGAbatch_Correction | Batch correction using ComBat and Voom transformation using limma package.
TCGAprepare_Affy | Prepare CEL files into an AffyBatch.
TCGAquery_MatchedCoupledSampleTypes | Retrieve multiple tissue types from the same patients.
TCGAquery_recount2 | Query gene counts of TCGA and GTEx data from the Recount2 project
TCGAquery_SampleTypes | Retrieve multiple tissue types not from the same patients.
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_meanMethylation | Mean methylation boxplot
TCGAvisualize_oncoprint | Creating a oncoprint
TCGAvisualize_PCA | Principal components analysis (PCA) plot
TCGAvisualize_starburst | Create starburst plot
TCGAvisualize_SurvivalCoxNET | Survival analysis with univariate Cox regression package (dnet)
TCGAVisualize_volcano | Creates a volcano plot for DNA methylation or gene expression
TCGA_MolecularSubtype | Retrieve molecular subtypes for given TCGA barcodes
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.