RTCGAToolbox: A new tool for exporting TCGA Firehose data
Version 1.0.1

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.

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AuthorMehmet Kemal Samur
Bioconductor views DifferentialExpression Sequencing
Date of publication2014-06-03 21:09:46
MaintainerMehmet Kemal Samur <samur@jimmy.harvard.edu>
LicenseGPL (>= 2)
Version1.0.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RTCGAToolbox", repos="http://R-Forge.R-project.org")

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...

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
RTCGASample Man page
RTCGAToolbox Man page
RTCGAToolbox-package Man page
getCNGECorrelation Man page Source code
getDiffExpressedGenes Man page Source code
getFirehoseAnalyzeDates Man page Source code
getFirehoseData Man page Source code
getFirehoseDatasets Man page Source code
getFirehoseRunningDates Man page Source code
getMutationRate Man page Source code
getReport Man page Source code
getSurvival Man page Source code
hg19.ucsc.gene.locations Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/RTCGAToolbox.R
data
data/RTCGASample.RData
data/datalist
data/hg19.ucsc.gene.locations.RData
inst
inst/CITATION
inst/NEWS
man
man/CorResult-class.Rd
man/DGEResult-class.Rd
man/FirehoseCGHArray-class.Rd
man/FirehoseData-class.Rd
man/FirehoseGISTIC-class.Rd
man/FirehoseMethylationArray-class.Rd
man/FirehosemRNAArray-class.Rd
man/RTCGASample.Rd
man/RTCGAToolbox-package.Rd
man/getCNGECorrelation.Rd
man/getDiffExpressedGenes.Rd
man/getFirehoseAnalyzeDates.Rd
man/getFirehoseData.Rd
man/getFirehoseDatasets.Rd
man/getFirehoseRunningDates.Rd
man/getMutationRate.Rd
man/getReport.Rd
man/getSurvival.Rd
man/hg19.ucsc.gene.locations.Rd
RTCGAToolbox documentation built on May 21, 2017, 1:07 a.m.