Man pages for BioinformaticsFMRP/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
chol_mafTCGA CHOL MAF transformed to maftools object
classificationResult of gliomaclassifier function
clinBRCAClinical data TCGA BRCA
clinical.biotabA list of data frames with clinical data parsed from XML...
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
DE_PCBC_stemSigA numeric vector with SC-derived definitive endoderm (DE)...
dmc.non.parametricPerform non-parametrix wilcoxon test
dmc.non.parametric.seCalculate pvalues
EB_PCBC_stemSigA numeric vector with stem cell (SC)-derived embryoid bodies...
ECTO_PCBC_stemSigA numeric vector with SC-derived ectoderm (ECTO) signature...
gaiaCNVplotCreates a plot for GAIA output (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_ATAC_seqRetrieve open access ATAC-seq files from GDC server
GDCquery_clinicGet GDC clinical data
geneInfogeneInfo for normalization of RNAseq data
geneInfoHTgeneInfoHT for normalization of HTseq data
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
get.GRCh.bioMartGet hg19 gene annotation or hg38 (gencode v36)
get_IDsExtract information from TCGA barcodes.
getLinkedOmicsDataRetrieve linkedOmics data
getManifestGet a Manifest from GDCquery output that can be used with...
getMC3MAFRetrieve open access mc3 MAF file from GDC server
getNbCasesGet Number of cases in GDC for a project
getNbFilesGet Number of files in GDC for a project
getProjectSummaryGet Project Summary from GDC
getResultsGet the results table from query
getSampleFilesSummaryRetrieve summary of files per sample in a project
getTSSgetTSS to fetch GENCODE gene annotation (transcripts level)...
ggbiplotBiplot for Principal Components using ggplot2
gliomaClassifierGliomar classifier
isServeOKCheck GDC server status is OK
matchedMetExpGet GDC primary tumors samples with both DNA methylation...
MESO_PCBC_stemSigA numeric vector with SC-derived mesoderm (MESO) signature...
met.gbm.27kA DNA methylation RangedSummarizedExperiment for 8 samples...
msi_resultsMSI data for two samples
pancan2018A data frame with all TCGA molecular subtypes
PanCancerAtlas_subtypesRetrieve table with TCGA molecular subtypes
SC_PCBC_stemSigA numeric vector with stem cell-like signature trained on...
splitAPICallinternal function to break a huge API call into smaller ones...
TabSubtypesCol_mergedTCGA samples with their Pam50 subtypes
TCGAanalyze_analyseGRNGenerate network
TCGAanalyze_ClusteringHierarchical cluster analysis
TCGAanalyze_DEADifferential expression analysis (DEA) using edgeR or limma...
TCGAanalyze_DEA_AffyDifferentially expression analysis (DEA) using limma package.
TCGAanalyze_DMCDifferentially 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_StemnessGenerate Stemness Score based on RNASeq (mRNAsi stemness...
TCGAanalyze_survivalCreates survival analysis
TCGAanalyze_SurvivalKMsurvival analysis (SA) univariate with Kaplan-Meier (KM)...
TCGAbatch_CorrectionBatch correction using ComBat and Voom transformation using...
TCGAbiolinks-packageThe aim of TCGAbiolinks is : i) facilitate the TCGA...
TCGA_MolecularSubtypeRetrieve molecular subtypes for given TCGA barcodes
TCGAprepare_AffyPrepare CEL files into an AffyBatch.
TCGAquery_MatchedCoupledSampleTypesRetrieve multiple tissue types from the same patients.
TCGAquery_recount2Query gene counts of TCGA and GTEx data from the Recount2...
TCGAquery_SampleTypesRetrieve multiple tissue types not from the same patients.
TCGAquery_subtypeRetrieve molecular subtypes for a given tumor
TCGAtumor_purityFilters TCGA barcodes according to purity parameters
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
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 gene expression
Tumor.purityTCGA samples with their Tumor Purity measures
UseRaw_afterFilterUse raw count from the DataPrep object which genes are...
BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.