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)
Version2.2.6
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

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

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