Registration Open for Bioc2024 July 24-26


A new tool for exporting TCGA Firehose data

Bioconductor version: Release (3.19)

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Author: Mehmet Samur [aut], Marcel Ramos [aut, cre] , Ludwig Geistlinger [ctb]

Maintainer: Marcel Ramos <marcel.ramos at>

Citation (from within R, enter citation("RTCGAToolbox")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

RTCGAToolbox Tutorial HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneExpression, Sequencing, Software
Version 2.34.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-2
Depends R (>= 4.3.0)
Imports BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors(>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils(>= 1.9.4), utils
System Requirements
Bug Reports
See More
Suggests BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
Linking To
Depends On Me
Imports Me cBioPortalData, TCGAWorkflow
Suggests Me TCGAutils
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RTCGAToolbox_2.34.0.tar.gz
Windows Binary
macOS Binary (x86_64) RTCGAToolbox_2.34.0.tgz
macOS Binary (arm64) RTCGAToolbox_2.34.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats