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.

Author
Mehmet Kemal Samur
Date of publication
None
Maintainer
Mehmet Kemal Samur <samur@jimmy.harvard.edu>
License
GPL (>= 2)
Version
2.4.0

View on Bioconductor

Man pages

CorResult-class
An S4 class to store correlations between gene expression...
DGEResult-class
An S4 class to store differential gene expression results
FirehoseCGHArray-class
An S4 class to store data from CGA platforms
FirehoseData-class
An S4 class to store main data object from clinent function.
FirehoseGISTIC-class
An S4 class to store processed copy number data. (Data...
FirehoseMethylationArray-class
An S4 class to store data from methylation platforms
FirehosemRNAArray-class
An S4 class to store data from array (mRNA, miRNA etc.)...
getCNGECorrelation
Perform correlation analysis betwwen gene expression and copy...
getData
Export data from FirehoseData object
getData-methods
Export data from FirehoseData object
getDiffExpressedGenes
Perform differential gene expression analysis for mRNA...
getFirehoseAnalyzeDates
Get data analyze dates.
getFirehoseData
Get data from Firehose portal.
getFirehoseDatasets
Get list of TCGA cohorts.
getFirehoseRunningDates
Get standard data running dates.
getMutationRate
Make a table for mutation rate of each gene in the cohort
getReport
Draws a circle plot into working directory
getSurvival
Perform survival analysis based on gene expression data
hg19.ucsc.gene.locations
Gene coordinates for circle plot.
RTCGASample
A sample data object for sample codes.
RTCGAToolbox
RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
showResults
Export toptable or correlation data frame
showResults-CorResult
Export toptable or correlation data frame
showResults-DGEResult
Export toptable or correlation data frame

Files in this package

RTCGAToolbox/DESCRIPTION
RTCGAToolbox/LICENSE
RTCGAToolbox/NAMESPACE
RTCGAToolbox/R
RTCGAToolbox/R/RTCGAToolbox-Class.R
RTCGAToolbox/R/RTCGAToolbox.R
RTCGAToolbox/R/getCNGECorrelation.R
RTCGAToolbox/R/getDiffExpressedGenes.R
RTCGAToolbox/R/getFirehoseAnalyzeDates.R
RTCGAToolbox/R/getFirehoseData.R
RTCGAToolbox/R/getFirehoseDatasets.R
RTCGAToolbox/R/getFirehoseRunningDates.R
RTCGAToolbox/R/getMutationRate.R
RTCGAToolbox/R/getReport.R
RTCGAToolbox/R/getSurvival.R
RTCGAToolbox/README.md
RTCGAToolbox/build
RTCGAToolbox/build/vignette.rds
RTCGAToolbox/data
RTCGAToolbox/data/RTCGASample.R
RTCGAToolbox/data/RTCGASample.RData
RTCGAToolbox/data/datalist
RTCGAToolbox/inst
RTCGAToolbox/inst/CITATION
RTCGAToolbox/inst/NEWS
RTCGAToolbox/inst/doc
RTCGAToolbox/inst/doc/RTCGAToolbox-vignette.R
RTCGAToolbox/inst/doc/RTCGAToolbox-vignette.Rmd
RTCGAToolbox/inst/doc/RTCGAToolbox-vignette.html
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.Rd
RTCGAToolbox/man/getCNGECorrelation.Rd
RTCGAToolbox/man/getData-methods.Rd
RTCGAToolbox/man/getData.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
RTCGAToolbox/man/showResults-CorResult.Rd
RTCGAToolbox/man/showResults-DGEResult.Rd
RTCGAToolbox/man/showResults.Rd
RTCGAToolbox/vignettes
RTCGAToolbox/vignettes/Figure2.png
RTCGAToolbox/vignettes/Figure3.png
RTCGAToolbox/vignettes/Figure4.png
RTCGAToolbox/vignettes/RTCGAToolbox-vignette.Rmd