[](https://travis-ci.org/BioinformaticsFMRP/TCGAbiolinks)
[](https://ci.appveyor.com/project/BioinformaticsFMRP/TCGAbiolinks)
[](https://codecov.io/github/BioinformaticsFMRP/TCGAbiolinks?branch=master)
[](http://bioconductor.org/packages/stats/bioc/TCGAbiolinks.html)
[](http://bioconductor.org/packages/TCGAbiolinks/)
[](http://bioconductor.org/packages/TCGAbiolinks/)
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# TCGAbiolinks - An R/Bioconductor package for integrative analysis with TCGA data
### Installation ###
```R
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
```
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### Docker image ###
TCGAbiolinks is available as Docker image (self-contained environments that contain everything needed to run the software),
which can be easily run on Mac OS, Windows and Linux systems.
This [PDF](https://drive.google.com/open?id=0B0-8N2fjttG-QXp5LVlPQnVQejg) show how to install and execute the image.
The image can be obtained from Docker Hub: https://hub.docker.com/r/tiagochst/tcgabiolinksgui/
For more information please check: https://docs.docker.com/ and https://www.bioconductor.org/help/docker/
### Manual ###
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html
http://bioinformaticsfmrp.github.io/TCGAbiolinks/
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## Citation
Please cite both TCGAbiolinks package:
* Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.
[](http://dx.doi.org/10.1093/nar/gkv1507) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=6029790855238928406) [](https://www.altmetric.com/details/4919535)
Also, if you have used ELMER analysis please cite:
* Yao, L., Shen, H., Laird, P. W., Farnham, P. J., & Berman, B. P. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome Biol 16 (2015): 105.
* Yao, Lijing, Benjamin P. Berman, and Peggy J. Farnham. "Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes." Critical reviews in biochemistry and molecular biology 50.6 (2015): 550-573.
