The family of R packages containing TCGA data

Data packages not yet submitted to Bioconductor from 2016-01-28 release date of TCGA data.

• RTCGA.mutations.20160128
• RTCGA.rnaseq.20160128
• RTCGA.clinical.20160128
• RTCGA.mRNA.20160128
• RTCGA.miRNASeq.20160128
• RTCGA.RPPA.20160128
• RTCGA.CNV.20160128
• RTCGA.methylation.20160128

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

• 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.

# 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.