TCGAbiolinks v1.2.5

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.

Readme

Build Status codecov.io bioc bioc bioc

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

Installation

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

Manual

http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html

Functions in TCGAbiolinks

Name Description
PR_status_BRCA PR_status_BRCA
TCGAvisualize_meanMethylation Mean methylation boxplot
TCGAanalyze_DEA_Affy Differentially expression analysis (DEA) using limma package.
TCGAvisualize_oncoprint Creating a oncoprint
TCGAquery_clinic Get the clinical information
TCGAprepare_Affy Prepare CEL files into an AffyBatch.
tabPackage2 tabPackage2
TCGAquery_subtype Retrieve molecular subtypes for a given tumor
TCGAquery_MatchedCoupledSampleTypes Retrieve multiple tissue types from the same patients.
TCGAprepare_elmer Prepare the data for ELEMR package
BRCA_rnaseqv2 BRCA_rnaseqv2
TCGAanalyze_SurvivalKM survival analysis (SA) univariate with Kaplan-Meier (KM) method.
TCGAvisualize_SurvivalCoxNET Survival analysis with univariate Cox regression package (dnet)
TCGAanalyze_EAcomplete Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways
dataREAD_df TCGA data matrix READ
tabSurvKMcompleteDEGs tabSurvKMcompleteDEGs
TCGAanalyze_Clustering Hierarchical cluster analysis
ER_status_BRCA ER_status_BRCA
HER_status_BRCA HER_status_BRCA
TCGAdownload Download the data from TCGA using as reference the output from TCGAquery
TCGAanalyze_Preprocessing Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier
TCGAanalyze_DMR Differentially methylated regions Analysis
TCGAvisualize_BarPlot Barplot of subtypes and clinical info in groups of gene expression clustered.
ggbiplot Biplot for Principal Components using ggplot2
geneInfo geneInfo for normalization
TCGAUpdate TCGAUpdate
TCGAvisualize_profilePlot Profile plot
TCGAbiolinks Download data of samples from TCGA
TCGAanalyze_EA Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.
diffmean Calculate diffmean methylation between two groups
TCGAanalyze_Filtering Filtering mRNA transcripts and miRNA selecting a threshold.
tabPackageKey tabPackageKey
TCGAquery_clinicFilt Filter samples using clinical data
TCGAquery_SampleTypes Retrieve multiple tissue types not from the same patients.
clinBRCA Clinical data TCGA BRCA
TCGAvisualize_Heatmap Heatmap with more sensible behavior using heatmap.plus
TCGAprepare Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.
dataBRCA TCGA data matrix BRCA
TCGAquery_maf Get last maf file for the tumor
gender_BRCA gender_BRCA
stage_BRCA stage_BRCA
TCGAvisualize_Tables Visaulize results in format of latex tables.
TCGAanalyze_DEA Differentially expression analysis (DEA) using edgeR package.
batch.info TCGA batch information from Biospecimen Metadata Browser
TCGAquery_Social Finds the number of downloads of a package on CRAN or BIOC and find questions in website ("bioconductor.org", "biostars.org", "stackoverflow).
TCGAvisualize_EAbarplot barPlot for a complete Enrichment Analysis
TCGAvisualize_starburst Create starburst plot
TCGAvisualize_PCA Principal components analysis (PCA) plot
tabDEGsTFPubmed TCGA data matrix BRCA DEGs Pubmed
BRCA_RNASeqV2_version TCGA Table with version, number of samples and size (Mbyte) of BRCA IlluminaHiSeq_RNASeqV2 Level 3
GeneSplitRegulon GeneSplitRegulon
TCGAVisualize_volcano Creates a volcano plot for DNA methylation or expression
TCGAanalyze_survival Creates survival analysis
TCGAquery_Version Shows a summary (version, date, number of samples, size of the data) of all versions of data for a given tumor and platform.
TCGAquery_samplesfilter Filtering sample output from TCGAquery
TCGAquery_integrate Filtering common samples among platforms from TCGAquery for the same tumor
TCGAvisualize_mutation Visualize mutation
dataDEGsFiltLevel TCGA data matrix BRCA DEGs
clinical_data_site_cancer clinical_data_site_cancer
calculate.pvalues Calculate pvalues
dataREAD TCGA data SummarizedExperiment READ
GenesCutID GenesCutID
TCGAanalyze_Normalization normalization mRNA transcripts and miRNA using EDASeq package.
TCGAquery_Investigate Find most studied TF in pubmed related to a specific cancer, disease, or tissue
TCGAquery Searches TCGA open-access data providing also latest version of the files.
TCGAanalyze_LevelTab Adding information related to DEGs genes from DEA as mean values in two conditions.
tabPackage1 tabPackage1
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