RTCGAToolbox: A new tool for exporting TCGA Firehose data

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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 Kemal Samur
Date of publication
2014-06-03 21:09:46
Maintainer
Mehmet Kemal Samur <samur@jimmy.harvard.edu>
License
GPL (>= 2)
Version
1.0.1

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Man pages

CorResult-class
Class '"CorResult"'
DGEResult-class
Class '"DGEResult"'
FirehoseCGHArray-class
Class '"FirehoseCGHArray"'
FirehoseData-class
Class '"FirehoseData"'
FirehoseGISTIC-class
Class '"FirehoseGISTIC"'
FirehoseMethylationArray-class
Class '"FirehoseMethylationArray"'
FirehosemRNAArray-class
Class '"FirehosemRNAArray"'
getCNGECorrelation
Correlation between copy number data and gene expression...
getDiffExpressedGenes
Get differentially expressed genes between tumor and normal...
getFirehoseAnalyzeDates
Firehose data analyze run dates
getFirehoseData
Firehose project data client
getFirehoseDatasets
Get valid dataset alias.
getFirehoseRunningDates
Get valid analysis dates.
getMutationRate
Calculates the mutation ratio among the samples.
getReport
Make report plot.
getSurvival
Survival analysis based on gene expression value.
hg19.ucsc.gene.locations
hg19 known gene symbol and locations
RTCGASample
Sample TCGA Firehose data from BRCA dataset.
RTCGAToolbox-package
RTCGAToolbox: A data client and basic analysis toolbox for...

Files in this package

RTCGAToolbox/DESCRIPTION
RTCGAToolbox/LICENSE
RTCGAToolbox/NAMESPACE
RTCGAToolbox/R
RTCGAToolbox/R/RTCGAToolbox.R
RTCGAToolbox/data
RTCGAToolbox/data/RTCGASample.RData
RTCGAToolbox/data/datalist
RTCGAToolbox/data/hg19.ucsc.gene.locations.RData
RTCGAToolbox/inst
RTCGAToolbox/inst/CITATION
RTCGAToolbox/inst/NEWS
RTCGAToolbox/man
RTCGAToolbox/man/CorResult-class.Rd
RTCGAToolbox/man/DGEResult-class.Rd
RTCGAToolbox/man/FirehoseCGHArray-class.Rd
RTCGAToolbox/man/FirehoseData-class.Rd
RTCGAToolbox/man/FirehoseGISTIC-class.Rd
RTCGAToolbox/man/FirehoseMethylationArray-class.Rd
RTCGAToolbox/man/FirehosemRNAArray-class.Rd
RTCGAToolbox/man/RTCGASample.Rd
RTCGAToolbox/man/RTCGAToolbox-package.Rd
RTCGAToolbox/man/getCNGECorrelation.Rd
RTCGAToolbox/man/getDiffExpressedGenes.Rd
RTCGAToolbox/man/getFirehoseAnalyzeDates.Rd
RTCGAToolbox/man/getFirehoseData.Rd
RTCGAToolbox/man/getFirehoseDatasets.Rd
RTCGAToolbox/man/getFirehoseRunningDates.Rd
RTCGAToolbox/man/getMutationRate.Rd
RTCGAToolbox/man/getReport.Rd
RTCGAToolbox/man/getSurvival.Rd
RTCGAToolbox/man/hg19.ucsc.gene.locations.Rd