devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")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 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/
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html http://bioinformaticsfmrp.github.io/TCGAbiolinks/
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.
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.