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RTCGAToolbox: a new tool for exporting TCGA Firehose data.

ABSTRACT:

Background & objective

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 the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data from the Firehouse, and demonstrate its use with sample case studies. Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data. The RTCGAToolbox can also be integrated with other analysis pipelines for further data processing.

Availability and implementation

The RTCGAToolbox is open-source and licensed under the GNU General Public License Version 2.0. All documentation and source code for RTCGAToolbox is freely available at http://mksamur.github.io/RTCGAToolbox/ for Linux and Mac OS X operating systems.

SUBMITTER: Samur MK

PROVIDER: S-EPMC4152273 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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RTCGAToolbox: a new tool for exporting TCGA Firehose data.

Samur Mehmet Kemal MK

PloS one 20140902 9

<h4>Background & objective</h4>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 the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data ...[more]

PMID: 25181531

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