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

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Documentation for package ‘TCGAbiolinks’ version 2.26.0

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

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 samples with both DNA methylation (HM450K) and Gene expression data from GDC databse
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.
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_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.