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# The family of R packages containing TCGA data
<img src="https://raw.githubusercontent.com/RTCGA/RTCGA/master/RTCGA_workflow.png" height="500" width="800">
Data packages **not yet** submitted to Bioconductor from 2016-01-28 release date of TCGA data.
- [RTCGA.mutations.20160128](http://github.com/RTCGA/RTCGA.mutations.20160128/)
- [RTCGA.rnaseq.20160128](http://github.com/RTCGA/RTCGA.rnaseq.20160128/)
- [RTCGA.clinical.20160128](http://github.com/RTCGA/RTCGA.clinical.20160128/)
- [RTCGA.mRNA.20160128](http://github.com/RTCGA/RTCGA.mRNA.20160128/)
- [RTCGA.miRNASeq.20160128](http://github.com/RTCGA/RTCGA.miRNASeq.20160128/)
- [RTCGA.RPPA.20160128](http://github.com/RTCGA/RTCGA.RPPA.20160128/)
- [RTCGA.CNV.20160128](http://github.com/RTCGA/RTCGA.CNV.20160128/)
- [RTCGA.methylation.20160128](http://github.com/RTCGA/RTCGA.methylation.20160128/)
Data packages submitted to Bioconductor from 2015-11-01 release date of TCGA data.
- [RTCGA.mutations](http://bioconductor.org/packages/RTCGA.mutations/)
- [RTCGA.rnaseq](http://bioconductor.org/packages/RTCGA.rnaseq/)
- [RTCGA.clinical](http://bioconductor.org/packages/RTCGA.clinical/)
- [RTCGA.PANCAN12](http://bioconductor.org/packages/RTCGA.PANCAN12/)
- [RTCGA.mRNA](http://bioconductor.org/packages/RTCGA.mRNA/)
- [RTCGA.miRNASeq](http://bioconductor.org/packages/RTCGA.miRNASeq/)
- [RTCGA.RPPA](http://bioconductor.org/packages/RTCGA.RPPA/)
- [RTCGA.CNV](http://bioconductor.org/packages/RTCGA.CNV/)
- [RTCGA.methylation](http://bioconductor.org/packages/RTCGA.methylation/)
### Installation of packages from the `RTCGA` family:
Windows users:
> Make sure you have [rtools](http://cran.r-project.org/bin/windows/Rtools/) installed on your computer.
```{R}
# 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`](https://github.com/RTCGA/RTCGA) package:
To get started, install the latest version of **RTCGA** from Bioconductor:
```{R}
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:
```{R}
if (!require(devtools)) {
install.packages("devtools")
require(devtools)
}
install_github("RTCGA/RTCGA", build_vignettes = TRUE)
```
To check Use Cases run
```{R}
browseVignettes("RTCGA")
```
<h4> Authors: </h4>
>
> 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.
