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

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.

AuthorAntonio 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
Date of publicationNone
MaintainerAntonio Colaprico <antonio.colaprico@ulb.ac.be>, Tiago Chedraoui Silva <tiagochst@usp.br>
LicenseGPL (>= 3)
Version2.2.10
https://github.com/BioinformaticsFMRP/TCGAbiolinks

View on Bioconductor

Man pages

batch.info: TCGA batch information from Biospecimen Metadata Browser

BRCA_rnaseqv2: BRCA_rnaseqv2

BRCA_RNASeqV2_version: TCGA Table with version, number of samples and size (Mbyte)...

calculate.pvalues: Calculate pvalues

clinBRCA: Clinical data TCGA BRCA

dataBRCA: TCGA data matrix BRCA

dataDEGsFiltLevel: TCGA data matrix BRCA DEGs

dataREAD: TCGA data SummarizedExperiment READ

dataREAD_df: TCGA data matrix READ

diffmean: Calculate diffmean methylation between two groups

GDCdownload: Download GDC data

GDCprepare: Prepare GDC data

GDCprepare_clinic: Parsing clinical xml files

GDCquery: Query GDC data

GDCquery_clinic: Get GDC clinical data

GDCquery_Maf: Retrieve open access maf files from GDC server

geneInfo: geneInfo for normalization of RNAseq data

geneInfoHT: geneInfoHT for normalization of HTseq data

GenesCutID: GenesCutID

GeneSplitRegulon: GeneSplitRegulon

getGDCprojects: Retrieve all GDC projects

getResults: Get the results table from query

ggbiplot: Biplot for Principal Components using ggplot2

isServeOK: Check GDC server status

tabDEGsTFPubmed: TCGA data matrix BRCA DEGs Pubmed

tabPackage1: tabPackage1

tabPackage2: tabPackage2

tabPackageKey: tabPackageKey

tabSurvKMcompleteDEGs: tabSurvKMcompleteDEGs

TCGAanalyze_analyseGRN: Generate network

TCGAanalyze_Clustering: Hierarchical cluster analysis

TCGAanalyze_DEA: Differentially expression analysis (DEA) using edgeR package.

TCGAanalyze_DEA_Affy: Differentially expression analysis (DEA) using limma package.

TCGAanalyze_DMR: Differentially methylated regions Analysis

TCGAanalyze_EA: Enrichment analysis of a gene-set with GO [BP,MF,CC] and...

TCGAanalyze_EAcomplete: Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and...

TCGAanalyze_Filtering: Filtering mRNA transcripts and miRNA selecting a threshold.

TCGAanalyze_LevelTab: Adding information related to DEGs genes from DEA as mean...

TCGAanalyze_networkInference: infer gene regulatory networks

TCGAanalyze_Normalization: normalization mRNA transcripts and miRNA using EDASeq...

TCGAanalyze_Pathview: Generate pathview graph

TCGAanalyze_Preprocessing: Array Array Intensity correlation (AAIC) and correlation...

TCGAanalyze_survival: Creates survival analysis

TCGAanalyze_SurvivalKM: survival analysis (SA) univariate with Kaplan-Meier (KM)...

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

TCGAprepare_Affy: Prepare CEL files into an AffyBatch.

TCGAprepare_elmer: Prepare the data for ELEMR package

TCGAquery_MatchedCoupledSampleTypes: Retrieve multiple tissue types from the same patients.

TCGAquery_SampleTypes: Retrieve multiple tissue types not from the same patients.

TCGAquery_subtype: Retrieve molecular subtypes for a given tumor

TCGAvisualize_BarPlot: Barplot of subtypes and clinical info in groups of gene...

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...

TCGAvisualize_Tables: Visaulize results in format of latex tables.

TCGAVisualize_volcano: Creates a volcano plot for DNA methylation or expression

Functions

batch.info Man page
BRCA_rnaseqv2 Man page
BRCA_RNASeqV2_version Man page
calculate.pvalues Man page
clinBRCA Man page
dataBRCA Man page
dataDEGsFiltLevel Man page
dataREAD Man page
dataREAD_df Man page
diffmean Man page
GDCdownload Man page
GDCprepare Man page
GDCprepare_clinic Man page
GDCquery Man page
GDCquery_clinic Man page
GDCquery_Maf Man page
geneInfo Man page
geneInfoHT Man page
GenesCutID Man page
GeneSplitRegulon Man page
getGDCprojects Man page
getResults Man page
ggbiplot Man page
isServeOK Man page
tabDEGsTFPubmed Man page
tabPackage1 Man page
tabPackage2 Man page
tabPackageKey Man page
tabSurvKMcompleteDEGs Man page
TCGAanalyze_analyseGRN Man page
TCGAanalyze_Clustering Man page
TCGAanalyze_DEA Man page
TCGAanalyze_DEA_Affy Man page
TCGAanalyze_DMR Man page
TCGAanalyze_EA Man page
TCGAanalyze_EAcomplete Man page
TCGAanalyze_Filtering Man page
TCGAanalyze_LevelTab Man page
TCGAanalyze_networkInference Man page
TCGAanalyze_Normalization Man page
TCGAanalyze_Pathview Man page
TCGAanalyze_Preprocessing Man page
TCGAanalyze_survival Man page
TCGAanalyze_SurvivalKM Man page
TCGAbiolinks Man page
TCGAbiolinks-package Man page
TCGAprepare_Affy Man page
TCGAprepare_elmer Man page
TCGAquery_MatchedCoupledSampleTypes Man page
TCGAquery_SampleTypes Man page
TCGAquery_subtype Man page
TCGAvisualize_BarPlot Man page
TCGAvisualize_EAbarplot Man page
TCGAvisualize_Heatmap Man page
TCGAvisualize_meanMethylation Man page
TCGAvisualize_oncoprint Man page
TCGAvisualize_PCA Man page
TCGAvisualize_starburst Man page
TCGAvisualize_SurvivalCoxNET Man page
TCGAvisualize_Tables Man page
TCGAVisualize_volcano Man page

Files

TCGAbiolinks/DESCRIPTION
TCGAbiolinks/NAMESPACE
TCGAbiolinks/NEWS
TCGAbiolinks/R
TCGAbiolinks/R/TCGADownload.R TCGAbiolinks/R/TCGAInternal.R TCGAbiolinks/R/TCGAPrepare.R TCGAbiolinks/R/TCGAQuery.R TCGAbiolinks/R/TCGAanalyze.R TCGAbiolinks/R/TCGAbiolinks.R TCGAbiolinks/R/TCGAquery_clinical.R TCGAbiolinks/R/TCGAvisualize.R TCGAbiolinks/R/methylation.R
TCGAbiolinks/R/sysdata.rda
TCGAbiolinks/README.md
TCGAbiolinks/build
TCGAbiolinks/build/vignette.rds
TCGAbiolinks/data
TCGAbiolinks/data/BRCA_RNASeqV2_version.rda
TCGAbiolinks/data/BRCA_rnaseqv2.rda
TCGAbiolinks/data/dataBRCA.rda
TCGAbiolinks/data/dataDEGsFiltLevel.rda
TCGAbiolinks/data/dataREAD.rda
TCGAbiolinks/data/dataREAD_df.rda
TCGAbiolinks/data/datalist
TCGAbiolinks/data/geneInfo.rda
TCGAbiolinks/data/geneInfoHT.rda
TCGAbiolinks/data/tabDEGsTFPubmed.rda
TCGAbiolinks/data/tabSurvKMcompleteDEGs.rda
TCGAbiolinks/inst
TCGAbiolinks/inst/CITATION
TCGAbiolinks/inst/doc
TCGAbiolinks/inst/doc/clinical.R
TCGAbiolinks/inst/doc/clinical.Rmd
TCGAbiolinks/inst/doc/clinical.html
TCGAbiolinks/inst/doc/download_prepare.R
TCGAbiolinks/inst/doc/download_prepare.Rmd
TCGAbiolinks/inst/doc/download_prepare.html
TCGAbiolinks/inst/doc/index.R
TCGAbiolinks/inst/doc/index.Rmd
TCGAbiolinks/inst/doc/index.html
TCGAbiolinks/inst/doc/mutation.R
TCGAbiolinks/inst/doc/mutation.Rmd
TCGAbiolinks/inst/doc/mutation.html
TCGAbiolinks/inst/doc/query.R
TCGAbiolinks/inst/doc/query.Rmd
TCGAbiolinks/inst/doc/query.html
TCGAbiolinks/inst/doc/tcgaBiolinks.R
TCGAbiolinks/inst/doc/tcgaBiolinks.Rmd
TCGAbiolinks/inst/doc/tcgaBiolinks.html
TCGAbiolinks/man
TCGAbiolinks/man/BRCA_RNASeqV2_version.Rd TCGAbiolinks/man/BRCA_rnaseqv2.Rd TCGAbiolinks/man/GDCdownload.Rd TCGAbiolinks/man/GDCprepare.Rd TCGAbiolinks/man/GDCprepare_clinic.Rd TCGAbiolinks/man/GDCquery.Rd TCGAbiolinks/man/GDCquery_Maf.Rd TCGAbiolinks/man/GDCquery_clinic.Rd TCGAbiolinks/man/GeneSplitRegulon.Rd TCGAbiolinks/man/GenesCutID.Rd TCGAbiolinks/man/TCGAVisualize_volcano.Rd TCGAbiolinks/man/TCGAanalyze_Clustering.Rd TCGAbiolinks/man/TCGAanalyze_DEA.Rd TCGAbiolinks/man/TCGAanalyze_DEA_Affy.Rd TCGAbiolinks/man/TCGAanalyze_DMR.Rd TCGAbiolinks/man/TCGAanalyze_EA.Rd TCGAbiolinks/man/TCGAanalyze_EAcomplete.Rd TCGAbiolinks/man/TCGAanalyze_Filtering.Rd TCGAbiolinks/man/TCGAanalyze_LevelTab.Rd TCGAbiolinks/man/TCGAanalyze_Normalization.Rd TCGAbiolinks/man/TCGAanalyze_Pathview.Rd TCGAbiolinks/man/TCGAanalyze_Preprocessing.Rd TCGAbiolinks/man/TCGAanalyze_SurvivalKM.Rd TCGAbiolinks/man/TCGAanalyze_analyseGRN.Rd TCGAbiolinks/man/TCGAanalyze_networkInference.Rd TCGAbiolinks/man/TCGAanalyze_survival.Rd TCGAbiolinks/man/TCGAbiolinks.Rd TCGAbiolinks/man/TCGAprepare_Affy.Rd TCGAbiolinks/man/TCGAprepare_elmer.Rd TCGAbiolinks/man/TCGAquery_MatchedCoupledSampleTypes.Rd TCGAbiolinks/man/TCGAquery_SampleTypes.Rd TCGAbiolinks/man/TCGAquery_subtype.Rd TCGAbiolinks/man/TCGAvisualize_BarPlot.Rd TCGAbiolinks/man/TCGAvisualize_EAbarplot.Rd TCGAbiolinks/man/TCGAvisualize_Heatmap.Rd TCGAbiolinks/man/TCGAvisualize_PCA.Rd TCGAbiolinks/man/TCGAvisualize_SurvivalCoxNET.Rd TCGAbiolinks/man/TCGAvisualize_Tables.Rd TCGAbiolinks/man/TCGAvisualize_meanMethylation.Rd TCGAbiolinks/man/TCGAvisualize_oncoprint.Rd TCGAbiolinks/man/TCGAvisualize_starburst.Rd TCGAbiolinks/man/batch.info.Rd TCGAbiolinks/man/calculate.pvalues.Rd TCGAbiolinks/man/clinBRCA.Rd TCGAbiolinks/man/dataBRCA.Rd TCGAbiolinks/man/dataDEGsFiltLevel.Rd TCGAbiolinks/man/dataREAD.Rd TCGAbiolinks/man/dataREAD_df.Rd TCGAbiolinks/man/diffmean.Rd TCGAbiolinks/man/geneInfo.Rd TCGAbiolinks/man/geneInfoHT.Rd TCGAbiolinks/man/getGDCprojects.Rd TCGAbiolinks/man/getResults.Rd TCGAbiolinks/man/ggbiplot.Rd TCGAbiolinks/man/isServeOK.Rd TCGAbiolinks/man/tabDEGsTFPubmed.Rd TCGAbiolinks/man/tabPackage1.Rd TCGAbiolinks/man/tabPackage2.Rd TCGAbiolinks/man/tabPackageKey.Rd TCGAbiolinks/man/tabSurvKMcompleteDEGs.Rd
TCGAbiolinks/tests
TCGAbiolinks/tests/testthat
TCGAbiolinks/tests/testthat.R
TCGAbiolinks/tests/testthat/test-analyse.R
TCGAbiolinks/tests/testthat/test-prepare-download.R
TCGAbiolinks/tests/testthat/test-query-clinical.R
TCGAbiolinks/tests/testthat/test-query.R
TCGAbiolinks/tests/testthat/test-visualize.R
TCGAbiolinks/vignettes
TCGAbiolinks/vignettes/BRCA_cluster.png
TCGAbiolinks/vignettes/BRCA_heatmap.png
TCGAbiolinks/vignettes/CIMP-highvsCIMP-low_metvolcano.png
TCGAbiolinks/vignettes/EAplot.png
TCGAbiolinks/vignettes/PCAtop200DEGs.png
TCGAbiolinks/vignettes/PreprocessingOutput.png
TCGAbiolinks/vignettes/SurvivalCoxNETOutput.png
TCGAbiolinks/vignettes/_output.yaml
TCGAbiolinks/vignettes/acc_mean.png
TCGAbiolinks/vignettes/case1_EA.png
TCGAbiolinks/vignettes/case1_dnet.png
TCGAbiolinks/vignettes/case2_Heatmap.png
TCGAbiolinks/vignettes/case2_surv.png
TCGAbiolinks/vignettes/case4_elmer.png
TCGAbiolinks/vignettes/clinical.Rmd
TCGAbiolinks/vignettes/download_prepare.Rmd
TCGAbiolinks/vignettes/elmer1.png
TCGAbiolinks/vignettes/elmer2.png
TCGAbiolinks/vignettes/elmer3.png
TCGAbiolinks/vignettes/elmer4.png
TCGAbiolinks/vignettes/figure4cluster.png
TCGAbiolinks/vignettes/figure4surv.png
TCGAbiolinks/vignettes/figure5exp.png
TCGAbiolinks/vignettes/figure5met.png
TCGAbiolinks/vignettes/figure5star.png
TCGAbiolinks/vignettes/include
TCGAbiolinks/vignettes/include/after_body.html
TCGAbiolinks/vignettes/include/before_body.html
TCGAbiolinks/vignettes/include/header.html
TCGAbiolinks/vignettes/include/logo.png
TCGAbiolinks/vignettes/include/site.css
TCGAbiolinks/vignettes/include/symbol.png
TCGAbiolinks/vignettes/index.Rmd
TCGAbiolinks/vignettes/libs
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TCGAbiolinks/vignettes/libs/dt-ext-fixedheader/css
TCGAbiolinks/vignettes/libs/dt-ext-fixedheader/css/fixedHeader.dataTables.min.css
TCGAbiolinks/vignettes/libs/dt-ext-fixedheader/js
TCGAbiolinks/vignettes/libs/dt-ext-fixedheader/js/dataTables.fixedHeader.min.js
TCGAbiolinks/vignettes/libs/dt-ext-keytable
TCGAbiolinks/vignettes/libs/dt-ext-keytable/css
TCGAbiolinks/vignettes/libs/dt-ext-keytable/css/keyTable.dataTables.min.css
TCGAbiolinks/vignettes/libs/dt-ext-keytable/js
TCGAbiolinks/vignettes/libs/dt-ext-keytable/js/dataTables.keyTable.min.js
TCGAbiolinks/vignettes/libs/dt-ext-responsive
TCGAbiolinks/vignettes/libs/dt-ext-responsive/css
TCGAbiolinks/vignettes/libs/dt-ext-responsive/css/responsive.dataTables.min.css
TCGAbiolinks/vignettes/libs/dt-ext-responsive/js
TCGAbiolinks/vignettes/libs/dt-ext-responsive/js/dataTables.responsive.min.js
TCGAbiolinks/vignettes/libs/dt-ext-rowreorder
TCGAbiolinks/vignettes/libs/dt-ext-rowreorder/css
TCGAbiolinks/vignettes/libs/dt-ext-rowreorder/css/rowReorder.dataTables.min.css
TCGAbiolinks/vignettes/libs/dt-ext-rowreorder/js
TCGAbiolinks/vignettes/libs/dt-ext-rowreorder/js/dataTables.rowReorder.min.js
TCGAbiolinks/vignettes/libs/dt-ext-scroller
TCGAbiolinks/vignettes/libs/dt-ext-scroller/css
TCGAbiolinks/vignettes/libs/dt-ext-scroller/css/scroller.dataTables.min.css
TCGAbiolinks/vignettes/libs/dt-ext-scroller/js
TCGAbiolinks/vignettes/libs/dt-ext-scroller/js/dataTables.scroller.min.js
TCGAbiolinks/vignettes/libs/dt-plugin-natural
TCGAbiolinks/vignettes/libs/dt-plugin-natural/natural.js
TCGAbiolinks/vignettes/libs/dt-plugin-searchhighlight
TCGAbiolinks/vignettes/libs/dt-plugin-searchhighlight/dataTables.searchHighlight.css
TCGAbiolinks/vignettes/libs/dt-plugin-searchhighlight/dataTables.searchHighlight.min.js
TCGAbiolinks/vignettes/libs/dt-plugin-searchhighlight/jquery.highlight.js
TCGAbiolinks/vignettes/libs/htmlwidgets
TCGAbiolinks/vignettes/libs/htmlwidgets/htmlwidgets.js
TCGAbiolinks/vignettes/libs/jquery
TCGAbiolinks/vignettes/libs/jquery-1.11.3
TCGAbiolinks/vignettes/libs/jquery-1.11.3/jquery.min.js
TCGAbiolinks/vignettes/libs/jquery/LICENSE.txt
TCGAbiolinks/vignettes/libs/jquery/jquery.min.js
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/README
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/images
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TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/images/ui-icons_555555_256x240.png
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/images/ui-icons_777620_256x240.png
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/images/ui-icons_777777_256x240.png
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/images/ui-icons_cc0000_256x240.png
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TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.css
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.js
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.min.css
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.min.js
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.structure.css
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.structure.min.css
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.theme.css
TCGAbiolinks/vignettes/libs/jqueryui-1.11.4/jquery-ui.theme.min.css
TCGAbiolinks/vignettes/libs/jszip
TCGAbiolinks/vignettes/libs/jszip/jszip.min.js
TCGAbiolinks/vignettes/libs/navigation-1.1
TCGAbiolinks/vignettes/libs/navigation-1.1/FileSaver.min.js
TCGAbiolinks/vignettes/libs/navigation-1.1/codefolding.js
TCGAbiolinks/vignettes/libs/navigation-1.1/sourceembed.js
TCGAbiolinks/vignettes/libs/navigation-1.1/tabsets.js
TCGAbiolinks/vignettes/libs/nouislider
TCGAbiolinks/vignettes/libs/nouislider/jquery.nouislider.min.css
TCGAbiolinks/vignettes/libs/nouislider/jquery.nouislider.min.js
TCGAbiolinks/vignettes/libs/pdfmake
TCGAbiolinks/vignettes/libs/pdfmake/pdfmake.min.js
TCGAbiolinks/vignettes/libs/pdfmake/vfs_fonts.js
TCGAbiolinks/vignettes/libs/selectize
TCGAbiolinks/vignettes/libs/selectize/selectize.bootstrap3.css
TCGAbiolinks/vignettes/libs/selectize/selectize.min.js
TCGAbiolinks/vignettes/libs/tocify-1.9.1
TCGAbiolinks/vignettes/libs/tocify-1.9.1/jquery.tocify.css
TCGAbiolinks/vignettes/libs/tocify-1.9.1/jquery.tocify.js
TCGAbiolinks/vignettes/mutation.Rmd
TCGAbiolinks/vignettes/oncoprint.png
TCGAbiolinks/vignettes/query.Rmd
TCGAbiolinks/vignettes/tcgaBiolinks.Rmd

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