Last data update: 2014.03.03
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RTCGAToolbox
Package: RTCGAToolbox
Type: Package
Title: A new tool for exporting TCGA Firehose data
Version: 2.2.2
Date: 2015-05-28
Author: Mehmet Kemal Samur
Maintainer: Mehmet Kemal Samur <samur@jimmy.harvard.edu>
Description: 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.
License: GPL (>= 2)
biocViews: Sequencing, DifferentialExpression, GeneExpression
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, Homo.sapiens
Imports: methods, XML, limma (>= 3.18), survival, RCircos, data.table (>=
1.9.4), RCurl, RJSONIO
Depends: R (>= 3.2.0)
NeedsCompilation: no
Packaged: 2016-05-16 05:28:21 UTC; biocbuild
● BiocViews: DifferentialExpression, GeneExpression, Sequencing
●
13 images,
24 functions,
0 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RTCGAToolbox' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'RTCGAToolbox'
finding HTML links ... done
CorResult-class html
DGEResult-class html
FirehoseCGHArray-class html
FirehoseData-class html
FirehoseGISTIC-class html
FirehoseMethylationArray-class html
FirehosemRNAArray-class html
RTCGASample html
RTCGAToolbox html
getCNGECorrelation html
getData-methods html
getData html
getDiffExpressedGenes html
getFirehoseAnalyzeDates html
getFirehoseData html
getFirehoseDatasets html
getFirehoseRunningDates html
getMutationRate html
getReport html
getSurvival html
hg19.ucsc.gene.locations html
showResults-CorResult html
showResults-DGEResult html
showResults html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGAToolbox)
Making 'packages.html' ... done
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