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

batch.infoTCGA batch information from Biospecimen Metadata Browser
bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.mafTCGA CHOL MAF
BRCA_rnaseqv2BRCA_rnaseqv2
calculate.pvaluesCalculate pvalues
chol_mafTCGA CHOL MAF transformed to maftools obejct
clinBRCAClinical data TCGA BRCA
colDataPrepareCreate samples information matrix for GDC samples
dataBRCATCGA data matrix BRCA
dataDEGsFiltLevelTCGA data matrix BRCA DEGs
dataREADTCGA data SummarizedExperiment READ
dataREAD_dfTCGA data matrix READ
diffmeanCalculate diffmean methylation between two groups
gaiaCNVplotCreates a plot for GAIA ouptut (all significant aberrant...
gbm.exp.harmonizedA RangedSummarizedExperiment two samples with gene expression...
gbm.exp.legacyA RangedSummarizedExperiment two samples with gene expression...
GDCdownloadDownload GDC data
GDCpreparePrepare GDC data
GDCprepare_clinicParsing clinical xml files
GDCqueryQuery GDC data
GDCquery_clinicGet GDC clinical data
GDCquery_MafRetrieve open access maf files from GDC server
geneInfogeneInfo for normalization of RNAseq data
geneInfoHTgeneInfoHT for normalization of HTseq data
GenesCutIDGenesCutID
GeneSplitRegulonGeneSplitRegulon
getAdjacencyBiogridGet a matrix of interactions of genes from biogrid
getDataCategorySummaryCreate a Summary table for each sample in a project saying if...
getGDCInfoCheck GDC server status
getGDCprojectsRetrieve all GDC projects
getGisticDownload GISTIC data from firehose
getResultsGet the results table from query
getTSSgetTSS to fetch GENCODE gene annotation (transcripts level)...
ggbiplotBiplot for Principal Components using ggplot2
isServeOKCheck GDC server status is OK
matchedMetExpGet GDC samples with both DNA methylation (HM450K) and Gene...
met.gbm.27kA DNA methylation RangedSummarizedExperiment for 8 samples...
msi_resultsMSI data for two samples
tabSurvKMcompleteDEGstabSurvKMcompleteDEGs
TCGAanalyze_analyseGRNGenerate network
TCGAanalyze_ClusteringHierarchical cluster analysis
TCGAanalyze_DEADifferentially expression analysis (DEA) using edgeR package.
TCGAanalyze_DEA_AffyDifferentially expression analysis (DEA) using limma package.
TCGAanalyze_DMRDifferentially methylated regions Analysis
TCGAanalyze_EAEnrichment analysis of a gene-set with GO [BP,MF,CC] and...
TCGAanalyze_EAcompleteEnrichment analysis for Gene Ontology (GO) [BP,MF,CC] and...
TCGAanalyze_FilteringFiltering mRNA transcripts and miRNA selecting a threshold.
TCGAanalyze_LevelTabAdding information related to DEGs genes from DEA as mean...
TCGAanalyze_networkInferenceinfer gene regulatory networks
TCGAanalyze_Normalizationnormalization mRNA transcripts and miRNA using EDASeq...
TCGAanalyze_PathviewGenerate pathview graph
TCGAanalyze_PreprocessingArray Array Intensity correlation (AAIC) and correlation...
TCGAanalyze_survivalCreates survival analysis
TCGAanalyze_SurvivalKMsurvival analysis (SA) univariate with Kaplan-Meier (KM)...
TCGAbiolinksThe aim of TCGAbiolinks is : i) facilitate the TCGA...
TCGAprepare_AffyPrepare CEL files into an AffyBatch.
TCGAquery_MatchedCoupledSampleTypesRetrieve multiple tissue types from the same patients.
TCGAquery_SampleTypesRetrieve multiple tissue types not from the same patients.
TCGAquery_subtypeRetrieve molecular subtypes for a given tumor
TCGAvisualize_BarPlotBarplot of subtypes and clinical info in groups of gene...
TCGAvisualize_EAbarplotbarPlot for a complete Enrichment Analysis
TCGAvisualize_HeatmapHeatmap with more sensible behavior using heatmap.plus
TCGAvisualize_meanMethylationMean methylation boxplot
TCGAvisualize_oncoprintCreating a oncoprint
TCGAvisualize_PCAPrincipal components analysis (PCA) plot
TCGAvisualize_starburstCreate starburst plot
TCGAvisualize_SurvivalCoxNETSurvival analysis with univariate Cox regression package...
TCGAVisualize_volcanoCreates a volcano plot for DNA methylation or expression
TCGAbiolinks documentation built on Dec. 8, 2017, 2:02 a.m.