Package: TCGAbiolinks 2.33.0

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_2.33.0.tar.gz
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TCGAbiolinks_2.33.0.tgz(r-4.4-any)TCGAbiolinks_2.33.0.tgz(r-4.3-any)
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TCGAbiolinks.pdf |TCGAbiolinks.html✨
TCGAbiolinks/json (API)
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Peer review:

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

On BioConductor:TCGAbiolinks-2.33.0(bioc 3.20)TCGAbiolinks-2.32.0(bioc 3.19)

bioconductor-package

57 exports 2.76 score 105 dependencies 6 dependents 276 mentions

Last updated 2 months agofrom:0ce7e26586

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