The Cancer Genome Atlas Data Integration • RTCGA (original) (raw)

Data packages 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 
# version of packages held at github.com/RTCGA 
# I try to keep them with the same state as devel versions of Bioconductor
library(RTCGA)
installTCGA("RTCGA.clinical.20160128")
installTCGA("RTCGA.mutations.20160128")
installTCGA("RTCGA.rnaseq.20160128")
installTCGA("RTCGA.CNV.20160128")
installTCGA("RTCGA.RPPA.20160128")
installTCGA("RTCGA.mRNA.20160128")
installTCGA("RTCGA.miRNASeq.20160128")
installTCGA("RTCGA.methylation.20160128")
installTCGA("RTCGA.PANCAN12")
installTCGA("RTCGA.clinical")
installTCGA("RTCGA.mutations")
installTCGA("RTCGA.rnaseq")
installTCGA("RTCGA.CNV")
installTCGA("RTCGA.RPPA")
installTCGA("RTCGA.mRNA")
installTCGA("RTCGA.miRNASeq")
installTCGA("RTCGA.methylation")
# or for all just type installTCGA()

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,

Przemysław Biecek,

Witold Chodor,

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

RTCGA logo