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TCGAbiolinks - An R/Bioconductor package for integrativ eanalysis with TCGA data

Installation

source("http://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

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Version

Version

1.0.10

License

GPL (>= 3)

Maintainer

Antonio Colaprico

Last Published

February 15th, 2017

Functions in TCGAbiolinks (1.0.10)

clinBRCA

Clinical data TCGA BRCA
BRCA_RNASeqV2_version

TCGA Table with version, number of samples and size (Mbyte) of BRCA IlluminaHiSeq_RNASeqV2 Level 3
dataBRCA

TCGA data matrix BRCA
dataREAD

TCGA data SummarizedExperiment READ
clinical_data_site_cancer

clinical_data_site_cancer
dataREAD_df

TCGA data matrix READ
batch.info

TCGA batch information from Biospecimen Metadata Browser
calculate.pvalues

Calculate pvalues
gender_BRCA

gender_BRCA
geneInfo

geneInfo for normalization
diffmean

Calculate diffmean methylation between two groups
ER_status_BRCA

ER_status_BRCA
ggbiplot

Biplot for Principal Components using ggplot2
GenesCutID

GenesCutID
HER_status_BRCA

HER_status_BRCA
GeneSplitRegulon

GeneSplitRegulon
tabPackage2

tabPackage2
tabPackageKey

tabPackageKey
TCGAanalyze_copynumber

Identifying Segment Gain Or Loss (SGOL)
TCGAanalyze_DEA_Affy

Differentially expression analysis (DEA) using limma package.
TCGAquery_Investigate

Find most studied TF in pubmed related to a specific cancer, disease, or tissue
TCGAquery_maf

Get last maf file for the tumor
TCGAvisualize_BarPlot

Barplot of subtypes and clinical info in groups of gene expression clustered.
TCGAvisualize_EAbarplot

barPlot for a complete Enrichment Analysis
TCGAVisualize_volcano

Creates a volcano plot for DNA methylation or expression
tabDEGsTFPubmed

TCGA data matrix BRCA DEGs Pubmed
tabPackage1

tabPackage1
TCGAanalyze_EA

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

Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways
TCGAquery_MatchedCoupledSampleTypes

Retrieve multiple tissue types from the same patients.
BRCA_rnaseqv2

BRCA_rnaseqv2
TCGAquery_samplesfilter

Filtering sample output from TCGAquery
tabSurvKMcompleteDEGs

tabSurvKMcompleteDEGs
stage_BRCA

stage_BRCA
PR_status_BRCA

PR_status_BRCA
TCGAdownload

Download the data from TCGA using as reference the output from TCGAquery
TCGAbiolinks

Download data of samples from TCGA
TCGAquery_clinicFilt

Filter samples using clinical data
TCGAanalyze_Clustering

Hierarchical cluster analysis
TCGAanalyze_Normalization

normalization mRNA transcripts and miRNA using EDASeq package.
TCGAvisualize_Heatmap

Heatmap with more sensible behavior using heatmap.plus
TCGAanalyze_Preprocessing

Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier
TCGAvisualize_meanMethylation

Mean methylation boxplot
TCGAanalyze_DEA

Differentially expression analysis (DEA) using edgeR package.
TCGAanalyze_DMR

Differentially methylated regions Analysis
TCGAanalyze_LevelTab

Adding information related to DEGs genes from DEA as mean values in two conditions.
TCGAanalyze_Filtering

Filtering mRNA transcripts and miRNA selecting a threshold.
TCGAprepare_Affy

Prepare CEL files into an AffyBatch.
TCGAquery

Searches TCGA open-access data providing also latest version of the files.
TCGAprepare_elmer

Prepare the data for ELEMR package
TCGAquery_integrate

Filtering common samples among platforms from TCGAquery for the same tumor
TCGAvisualize_PCA

Principal components analysis (PCA) plot
TCGAquery_subtype

Retrieve molecular subtypes for a given tumor
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.
TCGAvisualize_starburst

Create starburst plot
TCGAUpdate

TCGAUpdate
TCGAvisualize_SurvivalCoxNET

Survival analysis with univariate Cox regression package (dnet)
TCGAvisualize_Tables

Visaulize results in format of latex tables.
TCGAanalyze_survival

Creates survival analysis
dataDEGsFiltLevel

TCGA data matrix BRCA DEGs
TCGAanalyze_SurvivalKM

survival analysis (SA) univariate with Kaplan-Meier (KM) method.
TCGAprepare

Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.
TCGAquery_clinic

Get the clinical information
TCGAquery_SampleTypes

Retrieve multiple tissue types not from the same patients.
TCGAquery_Social

Finds the number of downloads of a package on CRAN or BIOC and find questions in website ("bioconductor.org", "biostars.org", "stackoverflow).