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

## Documentation for package ‘TCGAbiolinks’ version 2.5.9

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

## Help Pages

TCGAbiolinks-package | 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.
gaiaCNVplot | Creates a plot for GAIA ouptut (all significant aberrant regions.)
GDCdownload | Download GDC data
GDCprepare | Prepare GDC data
GDCprepare_clinic | Parsing clinical xml files
GDCquery | Query GDC data
GDCquery_clinic | Get GDC clinical data
GDCquery_Maf | Retrieve open access maf files from GDC server
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
TCGAanalyze_analyseGRN | Generate network
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_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_survival | Creates survival analysis
TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM) method.
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_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 expression