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 publicationNone
MaintainerMehmet Kemal Samur <samur@jimmy.harvard.edu>
LicenseGPL (>= 2)
Version2.4.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.