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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

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Version

Version

1.2.5

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/BioinformaticsFMRP/TCGAbiolinks

Maintainer

Antonio Colaprico

Last Published

February 15th, 2017

Functions in TCGAbiolinks (1.2.5)

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.

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

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

TCGA data matrix READ

tabSurvKMcompleteDEGs

tabSurvKMcompleteDEGs

TCGAanalyze_Clustering

Hierarchical cluster analysis

HER_status_BRCA

HER_status_BRCA

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.

Biplot for Principal Components using ggplot2

geneInfo for normalization

TCGAvisualize_profilePlot

Download data of samples from TCGA

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

Calculate diffmean methylation between two groups

TCGAanalyze_Filtering

Filtering mRNA transcripts and miRNA selecting a threshold.

TCGAquery_clinicFilt

Filter samples using clinical data

TCGAquery_SampleTypes

Retrieve multiple tissue types not from the same patients.

Clinical data TCGA BRCA

TCGAvisualize_Heatmap

Heatmap with more sensible behavior using heatmap.plus

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

TCGA data matrix BRCA

Get last maf file for the tumor

TCGAvisualize_Tables

Visaulize results in format of latex tables.

TCGAanalyze_DEA

Differentially expression analysis (DEA) using edgeR package.

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

TCGA data SummarizedExperiment READ

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

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.