README.md

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

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, [e-mail]

Przemysław Biecek, [e-mail]

Witold Chodor, [e-mail]

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

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.