README.md

In RTCGA: The Cancer Genome Atlas Data Integration

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
BiocManager::install(version = "devel") # swiches to devel branch of Bioconductor - don't use this line if you are interested in release versions
if (!requireNamespace("BiocManager", quietly=TRUE)) # downloads bioClite function
    install.packages("BiocManager") # downloads bioClite function

|package |installation |help |vignettes | |:-----------------|:-------------------------------|:--------------|:--------------------------------------| |RTCGA.rnaseq |BiocManager::install('RTCGA.rnaseq') |?rnaseq |browseVignettes('RTCGA.rnaseq') | |RTCGA.clinical |BiocManager::install('RTCGA.clinical') |?clinical |browseVignettes('RTCGA.clinical') | |RTCGA.mutations |BiocManager::install('RTCGA.mutations') |?mutations |browseVignettes('RTCGA.mutations') | |RTCGA.mRNA |BiocManager::install('RTCGA.mRNA') |?mRNA |browseVignettes('RTCGA.mRNA') | |RTCGA.miRNASeq |BiocManager::install('RTCGA.miRNASeq') |?miRNASeq |browseVignettes('RTCGA.miRNASeq') | |RTCGA.PANCAN12 |BiocManager::install('RTCGA.PANCAN12') |?pancan12 |browseVignettes('RTCGA.PANCAN12') | |RTCGA.RPPA |BiocManager::install('RTCGA.RPPA') |?RPPA |browseVignettes('RTCGA.RPPA') | |RTCGA.CNV |BiocManager::install('RTCGA.CNV') |?CNV |browseVignettes('RTCGA.CNV') | |RTCGA.methylation |BiocManager::install('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:

BiocManager::install(version = "devel") # swiches to devel branch of Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE)) # downloads bioClite function
    install.packages("BiocManager") # downloads bioClite function
BiocManager::install("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, [e-mail]

Przemysław Biecek, [e-mail]

Witold Chodor, [e-mail]

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

RTCGA documentation built on Nov. 8, 2020, 5:11 p.m.