TCGAbiolinks is able to access The National Cancer Institute (NCI) Genomic Data Commons (GDC) thorough its GDC Application Programming Interface (API) to search, download and prepare relevant data for analysis in R.
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("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/
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.
Mounir, Mohamed, Lucchetta, Marta, Silva, C T, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena (2019). “New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.” PLoS computational biology, 15(3), e1006701.
Silva TC, Colaprico A, Olsen C et al.TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]. F1000Research 2016, 5:1542 (https://doi.org/10.12688/f1000research.8923.2)
Also, if you have used ELMER analysis please cite:
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