Download, integration and visualizations of the variety & volume of TCGA data.
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README.md

Travis-CI Build Status Project Status: Active - The project has reached a stable, usable state and is being actively developed.Pending Pull-Requests Github Issues

The family of R packages containing TCGA data

Data packages that will be submitted to Bioconductor from 2016-01-28 release date of TCGA data.

Data packages submitted to Bioconductor from 2015-11-01 release date of TCGA data.

Installation of packages from the RTCGA family:

Windows users:

Make sure you have rtools installed on your computer.

# some packages might be still only available on the devel version of Bioconductor
BiocInstaller::useDevel() # swiches to devel branchof Bioconductor - don't use this line if you are interested in release versions
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
package installation help releaseDate
RTCGA.rnaseq.20160128 biocLite('RTCGA.rnaseq.20160128') ?rnaseq.20160128 2016-01-28
RTCGA.clinical.20160128 biocLite('RTCGA.clinical.20160128') ?clinical.20160128 2016-01-28
RTCGA.mutations.20160128 biocLite('RTCGA.mutations.20160128') ?mutations.20160128 2016-01-28
RTCGA.mRNA.20160128 biocLite('RTCGA.mRNA.20160128') ?mRNA.20160128 2016-01-28
RTCGA.miRNASeq.20160128 biocLite('RTCGA.miRNASeq.20160128') ?miRNASeq.20160128 2016-01-28
RTCGA.RPPA.20160128 biocLite('RTCGA.RPPA.20160128') ?RPPA.20160128 2016-01-28
RTCGA.CNV.20160128 biocLite('RTCGA.CNV.20160128') ?CNV.20160128 2016-01-28
RTCGA.methylation.20160128 biocLite('RTCGA.methylation.20160128') ?methylation.20160128 2016-01-28
RTCGA.rnaseq biocLite('RTCGA.rnaseq') ?rnaseq 2015-11-01
RTCGA.clinical biocLite('RTCGA.clinical') ?clinical 2015-11-01
RTCGA.mutations biocLite('RTCGA.mutations') ?mutations 2015-11-01
RTCGA.mRNA biocLite('RTCGA.mRNA') ?mRNA 2015-11-01
RTCGA.miRNASeq biocLite('RTCGA.miRNASeq') ?miRNASeq 2015-11-01
RTCGA.PANCAN12 biocLite('RTCGA.PANCAN12') ?pancan12 NULL
RTCGA.RPPA biocLite('RTCGA.RPPA') ?RPPA 2015-11-01
RTCGA.CNV biocLite('RTCGA.CNV') ?CNV 2015-11-01
RTCGA.methylation biocLite('RTCGA.methylation') ?methylation 2015-11-01

RTCGA

Packages from the RTCGA.data - family/factory are based on the RTCGA package

Installation of the RTCGA package:

To get started, install the latest version of RTCGA from Bioconductor:

BiocInstaller::useDevel() # swiches to devel branch of Bioconductor
source("https://bioconductor.org/biocLite.R") # downloads bioClite function
biocLite("RTCGA") # installs a package

or use below code to download the development version which is like to be less bugged than the release version on Bioconductor:

if (!require(devtools)) {
    install.packages("devtools")
    require(devtools)
}
install_github("RTCGA/RTCGA", build_vignettes = TRUE)

To check Use Cases run

browseVignettes("RTCGA")

Authors:

Marcin Kosiński, m.p.kosinski@gmail.com

Przemysław Biecek, przemyslaw.biecek@gmail.com

Witold Chodor, witoldchodor@gmail.com

This repository is synchronized with it's Bioconductor's SVN devel mirror.

RTCGA logo