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

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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.

Author
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
Date of publication
None
Maintainer
Antonio Colaprico <antonio.colaprico@ulb.ac.be>, Tiago Chedraoui Silva <tiagochst@usp.br>
License
GPL (>= 3)
Version
2.2.6
URLs

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
ER_status_BRCA
ER_status_BRCA
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
gender_BRCA
gender_BRCA
geneInfo
geneInfo for normalization
GenesCutID
GenesCutID
GeneSplitRegulon
GeneSplitRegulon
getGDCprojects
Retrieve all GDC projects
ggbiplot
Biplot for Principal Components using ggplot2
HER_status_BRCA
HER_status_BRCA
isServeOK
Check GDC server status
PR_status_BRCA
PR_status_BRCA
stage_BRCA
stage_BRCA
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_Normalization
normalization mRNA transcripts and miRNA using EDASeq...
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_clinicFilt
Filter samples using clinical data
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

Files in this package

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/tabDEGsTFPubmed.rda
TCGAbiolinks/data/tabSurvKMcompleteDEGs.rda
TCGAbiolinks/inst
TCGAbiolinks/inst/CITATION
TCGAbiolinks/inst/doc
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/ER_status_BRCA.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/HER_status_BRCA.Rd
TCGAbiolinks/man/PR_status_BRCA.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_Preprocessing.Rd
TCGAbiolinks/man/TCGAanalyze_SurvivalKM.Rd
TCGAbiolinks/man/TCGAanalyze_analyseGRN.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_clinicFilt.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/gender_BRCA.Rd
TCGAbiolinks/man/geneInfo.Rd
TCGAbiolinks/man/getGDCprojects.Rd
TCGAbiolinks/man/ggbiplot.Rd
TCGAbiolinks/man/isServeOK.Rd
TCGAbiolinks/man/stage_BRCA.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/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/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/oncoprint.png
TCGAbiolinks/vignettes/tcgaBiolinks.Rmd