recipe bioconductor-rtcgatoolbox

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.







biotools: rtcgatoolbox

package bioconductor-rtcgatoolbox

(downloads) docker_bioconductor-rtcgatoolbox


2.12.1-0, 2.10.0-0, 2.8.0-0, 2.6.0-0

Depends bioconductor-biocgenerics


Depends bioconductor-delayedarray


Depends bioconductor-genomeinfodb


Depends bioconductor-genomicranges


Depends bioconductor-iranges


Depends bioconductor-limma


Depends bioconductor-raggedexperiment


Depends bioconductor-s4vectors


Depends bioconductor-summarizedexperiment


Depends bioconductor-tcgautils


Depends r-base


Depends r-data.table

Depends r-rcircos

Depends r-rcurl

Depends r-rjsonio

Depends r-stringr

Depends r-survival

Depends r-xml



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-rtcgatoolbox

and update with:

conda update bioconductor-rtcgatoolbox

or use the docker container:

docker pull<tag>

(see bioconductor-rtcgatoolbox/tags for valid values for <tag>)