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RTCGAToolbox: a new tool for exporting TCGA Firehose data.

Mehmet Kemal Samur¹

¹Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, United States of America; Lebow Institute of Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America.

|September 3, 2014

Summary

Researchers can now more easily manage and analyze The Cancer Genome Atlas (TCGA) data using RTCGAToolbox, an open-source R package. This tool simplifies data handling for large-scale cancer genomics projects.

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Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Managing large-scale project data, like The Cancer Genome Atlas (TCGA), is crucial but time-consuming for researchers.
Existing resources like the Firehose project provide TCGA data, but require significant effort for management, download, and preparation.

Purpose of the Study:

To develop an open-source, extensible R-based data client for accessing and managing pre-processed TCGA data.
To demonstrate the utility of this tool through sample case studies, facilitating data management for researchers.

Main Methods:

Developed RTCGAToolbox, an open-source R package.
The tool is licensed under the GNU General Public License Version 2.0.
Documentation and source code are available online for Linux and Mac OS X.

Main Results:

RTCGAToolbox effectively facilitates data management for researchers working with TCGA data.
The tool streamlines the process of accessing and preparing pre-processed TCGA datasets.
Demonstrated successful integration with other analysis pipelines for further data processing.

Conclusions:

RTCGAToolbox offers a valuable solution for simplifying TCGA data management.
The open-source nature and extensibility of RTCGAToolbox promote broader adoption and integration in cancer research.
This tool empowers researchers to more efficiently utilize large-scale cancer genomics data for analysis.