Last data update: 2014.03.03


Package: RTCGA
Title: The Cancer Genome Atlas Data Integration
Version: 1.2.2
Date: 2016-03-30
Author: Marcin Kosinski <>, Przemyslaw Biecek
Maintainer: Marcin Kosinski <>
Description: The Cancer Genome Atlas (TCGA) Data Portal provides a
platform for researchers to search, download, and analyze data
sets generated by TCGA. It contains clinical information,
genomic characterization data, and high level sequence analysis
of the tumor genomes. The key is to understand genomics to
improve cancer care. RTCGA package offers download and
integration of the variety and volume of TCGA data using
patient barcode key, what enables easier data possession. This
may have an benefcial infuence on impact on development of
science and improvement of patients' treatment. Furthermore,
RTCGA package transforms TCGA data to tidy form which is
convenient to use.
License: GPL-2
LazyLoad: yes
LazyData: yes
Depends: R (>= 3.2.0)
Imports: XML, assertthat, stringi, rvest, data.table, xml2, devtools,
dplyr, purrr, knitr, survival, survminer, ggplot2, ggthemes,
viridis, scales
Suggests: testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors,
RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA,
RTCGA.PANCAN12, magrittr, tidyr
Repository: Bioconductor
biocViews: Software, DataImport, DataRepresentation, Preprocessing
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:39:45 UTC; biocbuild

● BiocViews: DataImport, DataRepresentation, Preprocessing, Software
29 images, 16 functions, 0 datasets
Reverse Depends: 9

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RTCGA' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCGA'
    finding HTML links ... done
    RTCGA-package                           html  
    boxplotTCGA                             html  
    finding level-2 HTML links ... done

    checkTCGA                               html  
    convertTCGA                             html  
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:23: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:23: missing file link 'GRanges'
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:13: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:13: missing file link 'GRanges'
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:18: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpGi7SHm/R.INSTALL3ef54be483c4/RTCGA/man/convertTCGA.Rd:18: missing file link 'GRanges'
    datasetsTCGA                            html  
    downloadTCGA                            html  
    expressionsTCGA                         html  
    heatmapTCGA                             html  
    infoTCGA                                html  
    installTCGA                             html  
    kmTCGA                                  html  
    mutationsTCGA                           html  
    pcaTCGA                                 html  
    readTCGA                                html  
    survivalTCGA                            html  
    theme_RTCGA                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Making 'packages.html' ... done