RTCGAToolbox: A new tool for exporting TCGA Firehose data

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.

AuthorMehmet Kemal Samur
Date of publication2014-06-03 21:09:46
MaintainerMehmet Kemal Samur <samur@jimmy.harvard.edu>
LicenseGPL (>= 2)
Version1.0.1

View on R-Forge

Functions

CorResult-class Man page
DGEResult-class Man page
FirehoseCGHArray-class Man page
FirehoseData-class Man page
FirehoseGISTIC-class Man page
FirehoseMethylationArray-class Man page
FirehosemRNAArray-class Man page
getCNGECorrelation Man page
getDiffExpressedGenes Man page
getFirehoseAnalyzeDates Man page
getFirehoseData Man page
getFirehoseDatasets Man page
getFirehoseRunningDates Man page
getMutationRate Man page
getReport Man page
getSurvival Man page
hg19.ucsc.gene.locations Man page
RTCGASample Man page
RTCGAToolbox Man page
RTCGAToolbox-package Man page

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