Last data update: 2014.03.03
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RTCGA
Package: RTCGA
Title: The Cancer Genome Atlas Data Integration
Version: 1.2.2
Date: 2016-03-30
Author: Marcin Kosinski <m.p.kosinski@gmail.com>, Przemyslaw Biecek
<przemyslaw.biecek@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
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.
BugReports: https://github.com/RTCGA/RTCGA/issues
URL: https://rtcga.github.io/RTCGA
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.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV,
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
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
* DONE (RTCGA)
Making 'packages.html' ... done
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