Package: TCGAbiolinks 2.35.0

Tiago Chedraoui Silva

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

The aim of TCGAbiolinks is : i) facilitate the GDC 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) 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.

Authors:Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr

TCGAbiolinks_2.35.0.tar.gz
TCGAbiolinks_2.35.0.zip(r-4.5)TCGAbiolinks_2.35.0.zip(r-4.4)TCGAbiolinks_2.35.0.zip(r-4.3)
TCGAbiolinks_2.35.0.tgz(r-4.4-any)TCGAbiolinks_2.35.0.tgz(r-4.3-any)
TCGAbiolinks_2.35.0.tar.gz(r-4.5-noble)TCGAbiolinks_2.35.0.tar.gz(r-4.4-noble)
TCGAbiolinks_2.35.0.tgz(r-4.4-emscripten)TCGAbiolinks_2.35.0.tgz(r-4.3-emscripten)
TCGAbiolinks.pdf |TCGAbiolinks.html✨
TCGAbiolinks/json (API)
NEWS

# Install 'TCGAbiolinks' in R:
install.packages('TCGAbiolinks', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioinformaticsfmrp/tcgabiolinks/issues

Datasets:

On BioConductor:TCGAbiolinks-2.35.0(bioc 3.21)TCGAbiolinks-2.34.0(bioc 3.20)

dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks

12.51 score 300 stars 6 packages 1.6k scripts 6.9k downloads 276 mentions 57 exports 105 dependencies

Last updated 2 months agofrom:cd39121b7f. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 19 2024
R-4.5-winERRORDec 19 2024
R-4.5-linuxERRORDec 19 2024
R-4.4-winERRORDec 19 2024
R-4.4-macERRORDec 19 2024
R-4.3-winERRORDec 19 2024
R-4.3-macERRORDec 19 2024

Exports:colDataPreparegaiaCNVplotGDCdownloadGDCprepareGDCprepare_clinicGDCqueryGDCquery_ATAC_seqGDCquery_clinicget_IDsget.GRCh.bioMartgetAdjacencyBiogridgetDataCategorySummarygetGDCInfogetGDCprojectsgetGisticgetLinkedOmicsDatagetManifestgetMC3MAFgetProjectSummarygetResultsgetSampleFilesSummarygliomaClassifierisServeOKmatchedMetExpPanCancerAtlas_subtypesTCGA_MolecularSubtypeTCGAanalyze_analyseGRNTCGAanalyze_ClusteringTCGAanalyze_DEATCGAanalyze_DEA_AffyTCGAanalyze_DMCTCGAanalyze_EAcompleteTCGAanalyze_FilteringTCGAanalyze_LevelTabTCGAanalyze_networkInferenceTCGAanalyze_NormalizationTCGAanalyze_PathviewTCGAanalyze_PreprocessingTCGAanalyze_StemnessTCGAanalyze_survivalTCGAanalyze_SurvivalKMTCGAbatch_CorrectionTCGAprepare_AffyTCGAquery_MatchedCoupledSampleTypesTCGAquery_recount2TCGAquery_SampleTypesTCGAquery_subtypeTCGAtumor_purityTCGAvisualize_BarPlotTCGAvisualize_EAbarplotTCGAvisualize_HeatmapTCGAvisualize_meanMethylationTCGAvisualize_oncoprintTCGAvisualize_PCATCGAvisualize_starburstTCGAVisualize_volcanoUseRaw_afterFilter

Dependencies:abindAnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicliprcolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdownloaderdplyrevaluatefansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshttrhttr2IRangesisobandjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrlangRSQLitervestS4ArraysS4VectorsscalesselectrSparseArraystringistringrSummarizedExperimentsysTCGAbiolinksGUI.datatibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Create samples information matrix for GDC samplescolDataPrepare
Perform non-parametrix wilcoxon testdmc.non.parametric
Creates a plot for GAIA output (all significant aberrant regions.)gaiaCNVplot
Download GDC dataGDCdownload
Prepare GDC dataGDCprepare
Parsing clinical xml filesGDCprepare_clinic
Query GDC dataGDCquery
Retrieve open access ATAC-seq files from GDC serverGDCquery_ATAC_seq
Get GDC clinical dataGDCquery_clinic
Extract information from TCGA barcodes.get_IDs
Get hg19 gene annotation or hg38 (gencode v36)get.GRCh.bioMart
Get a matrix of interactions of genes from biogridgetAdjacencyBiogrid
Create a Summary table for each sample in a project saying if it contains or not files for a certain data categorygetDataCategorySummary
Check GDC server statusgetGDCInfo
Retrieve all GDC projectsgetGDCprojects
Download GISTIC data from firehosegetGistic
Retrieve linkedOmics datagetLinkedOmicsData
Get a Manifest from GDCquery output that can be used with GDC-clientgetManifest
Retrieve open access mc3 MAF file from GDC servergetMC3MAF
Get Number of cases in GDC for a projectgetNbCases
Get Number of files in GDC for a projectgetNbFiles
Get Project Summary from GDCgetProjectSummary
Get the results table from querygetResults
Retrieve summary of files per sample in a projectgetSampleFilesSummary
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.getTSS
Gliomar classifiergliomaClassifier
Check GDC server status is OKisServeOK
Get GDC primary tumors samples with both DNA methylation (HM450K) and Gene expression datamatchedMetExp
Retrieve table with TCGA molecular subtypesPanCancerAtlas_subtypes
internal function to break a huge API call into smaller ones so it repects the max character limit of a stringsplitAPICall
TCGA samples with their Pam50 subtypesTabSubtypesCol_merged
Retrieve molecular subtypes for given TCGA barcodesTCGA_MolecularSubtype
Generate networkTCGAanalyze_analyseGRN
Hierarchical cluster analysisTCGAanalyze_Clustering
Differential expression analysis (DEA) using edgeR or limma package.TCGAanalyze_DEA
Differentially expression analysis (DEA) using limma package.TCGAanalyze_DEA_Affy
Differentially methylated regions AnalysisTCGAanalyze_DMC
Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.TCGAanalyze_EA
Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and PathwaysTCGAanalyze_EAcomplete
Filtering mRNA transcripts and miRNA selecting a threshold.TCGAanalyze_Filtering
Adding information related to DEGs genes from DEA as mean values in two conditions.TCGAanalyze_LevelTab
infer gene regulatory networksTCGAanalyze_networkInference
normalization mRNA transcripts and miRNA using EDASeq package.TCGAanalyze_Normalization
Generate pathview graphTCGAanalyze_Pathview
Array Array Intensity correlation (AAIC) and correlation boxplot to define outlierTCGAanalyze_Preprocessing
Generate Stemness Score based on RNASeq (mRNAsi stemness index) Malta et al., Cell, 2018TCGAanalyze_Stemness
Creates survival analysisTCGAanalyze_survival
survival analysis (SA) univariate with Kaplan-Meier (KM) method.TCGAanalyze_SurvivalKM
Batch correction using ComBat and Voom transformation using limma package.TCGAbatch_Correction
Prepare CEL files into an AffyBatch.TCGAprepare_Affy
Retrieve multiple tissue types from the same patients.TCGAquery_MatchedCoupledSampleTypes
Query gene counts of TCGA and GTEx data from the Recount2 projectTCGAquery_recount2
Retrieve multiple tissue types not from the same patients.TCGAquery_SampleTypes
Retrieve molecular subtypes for a given tumorTCGAquery_subtype
Filters TCGA barcodes according to purity parametersTCGAtumor_purity
Barplot of subtypes and clinical info in groups of gene expression clustered.TCGAvisualize_BarPlot
barPlot for a complete Enrichment AnalysisTCGAvisualize_EAbarplot
Heatmap with more sensible behavior using heatmap.plusTCGAvisualize_Heatmap
Mean methylation boxplotTCGAvisualize_meanMethylation
Creating a oncoprintTCGAvisualize_oncoprint
Principal components analysis (PCA) plotTCGAvisualize_PCA
Create starburst plotTCGAvisualize_starburst
Survival analysis with univariate Cox regression package (dnet)TCGAvisualize_SurvivalCoxNET
Creates a volcano plot for DNA methylation or gene expressionTCGAVisualize_volcano
TCGA samples with their Tumor Purity measuresTumor.purity
Use raw count from the DataPrep object which genes are removed by normalization and filtering steps.UseRaw_afterFilter