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


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Documentation for package ‘TCGAbiolinks’ version 2.0.13

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TCGAbiolinks-package Download data of samples from TCGA
GDCdownload Download GDC data
GDCprepare Prepare GDC data
GDCprepare_clinic Parsing clinical xml files
GDCquery Query GDC data
GDCquery_clinic Get DDC clinical data
GDCquery_Maf Retrieve open access maf files from GDC server
getGDCprojects Retrieve all GDC projects
isServeOK Check GDC server status
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_Normalization normalization mRNA transcripts and miRNA using EDASeq package.
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 Download data of samples from TCGA
TCGAdownload Download the data from TCGA using as reference the output from TCGAquery
TCGAprepare Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.
TCGAprepare_Affy Prepare CEL files into an AffyBatch.
TCGAprepare_elmer Prepare the data for ELEMR package
TCGAquery Searches TCGA open-access data providing also latest version of the files.
TCGAquery_clinic Get the clinical information
TCGAquery_clinicFilt Filter samples using clinical data
TCGAquery_maf Get last maf file for the tumor
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_Tables Visaulize results in format of latex tables.
TCGAVisualize_volcano Creates a volcano plot for DNA methylation or expression