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 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| package | installation | help | vignettes |
|---|---|---|---|
| RTCGA.rnaseq | biocLite('RTCGA.rnaseq') | ?rnaseq | browseVignettes('RTCGA.rnaseq') |
| RTCGA.clinical | biocLite('RTCGA.clinical') | ?clinical | browseVignettes('RTCGA.clinical') |
| RTCGA.mutations | biocLite('RTCGA.mutations') | ?mutations | browseVignettes('RTCGA.mutations') |
| RTCGA.mRNA | biocLite('RTCGA.mRNA') | ?mRNA | browseVignettes('RTCGA.mRNA') |
| RTCGA.miRNASeq | biocLite('RTCGA.miRNASeq') | ?miRNASeq | browseVignettes('RTCGA.miRNASeq') |
| RTCGA.PANCAN12 | biocLite('RTCGA.PANCAN12') | ?pancan12 | browseVignettes('RTCGA.PANCAN12') |
| RTCGA.RPPA | biocLite('RTCGA.RPPA') | ?RPPA | browseVignettes('RTCGA.RPPA') |
| RTCGA.CNV | biocLite('RTCGA.CNV') | ?CNV | browseVignettes('RTCGA.CNV') |
| RTCGA.methylation | biocLite('RTCGA.methylation') | ?methylation | browseVignettes('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()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 packageor 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")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.