Last data update: 2014.03.03

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