The family of R packages containing TCGA data
Data packages submitted to Bioconductor
- RTCGA.mutations
- RTCGA.rnaseq
- RTCGA.clinical
- RTCGA.PANCAN12
- RTCGA.mRNA
- RTCGA.miRNASeq
- RTCGA.RPPA
- RTCGA.CNV
- RTCGA.methylation
Installation of packages from the RTCGA.data family:
Windows users:
Make sure you have rtools installed on your computer.
# packages that are published to 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
biocLite("RTCGA.clinical") # installs a package
biocLite("RTCGA.rnaseq")
biocLite("RTCGA.mutations")
biocLite("RTCGA.PANCAN12")
biocLite("RTCGA.CNV")
biocLite("RTCGA.RPPA")
biocLite("RTCGA.mRNA")
biocLite("RTCGA.miRNASeq")
biocLite("RTCGA.methylation")
# 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.PANCAN12")
installTCGA("RTCGA.CNV")
installTCGA("RTCGA.RPPA")
installTCGA("RTCGA.mRNA")
installTCGA("RTCGA.miRNASeq")
installTCGA("RTCGA.methylation")
# or for all just type installTCGA()
The list of available datasets:
```{R} help(dataType) # where dataType is one of: 'datasetsTCGA', 'clinical', 'rnaseq' # 'mutations', 'pancan12', 'CNV', 'RPPA', 'mRNA', 'miRNASeq', 'methylation' ```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, [email protected]
Przemysław Biecek, [email protected]
Witold Chorod, [email protected]
This repository is synchronized with it's Bioconductor's SVN devel mirror.
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