TCGAbiolinksGUI was created to help users more comfortable with
graphical user interfaces (GUI) to search, download and analyze Cancer
data. It offers a graphical user interface to the R/Bioconductor package
TCGAbiolinks
(Colaprico et al. 2016), which is able to
access The National Cancer Institute (NCI) Genomic Data Commons (GDC)
through its
GDC
Application Programming Interface (API). Additional packages from
Bioconductor are included, such as maftools (Mayakonda et al. 2018) and ComplexHeatmap
(Gu, Eils, and Schlesner 2016) packages to
aid in visualizing the mutation data, ELMER (Yao et al. 2015) to identify regulatory
enhancers using gene expression + DNA methylation data + motif analysis,
Pathview (Luo and Brouwer 2013) for pathway-based data
integration and visualization, and minfi for the
processing of DNA methylation raw idat files.
The GUI was created using Shiny, a Web Application Framework for R, and uses several packages to provide advanced features that can enhance Shiny apps, such as shinyjs to add JavaScript actions for the app, shinydashboard to add dashboards and shinyFiles to provide an API for client side access to the server file system. A running version of the GUI is found in http://tcgabiolinks.fmrp.usp.br:3838/
This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the São Paulo Research Foundation FAPESP (2016/01389-7 to T.C.S. & H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O. & G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826.
To install the package from the Bioconductor repository please use the following code.
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
::install("TCGAbiolinksGUI", dependencies = TRUE) BiocManager
To install the development version of the package via GitHub:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
::install_github("BioinformaticsFMRP/TCGAbiolinksGUI.data",ref = "R_3.4")
devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI") devtools
If you receive this error message:
maximal number of DLLs reached...
You will need to increase
the maximum number of DLL R can load wit the environment variable
R_MAX_NUM_DLLS
.
For MACOS please modify the file
/Library/Frameworks/R.framework/Resources/etc/Renviron
and
add R_MAX_NUM_DLLS=150
in the end. Or you can run in R the
following command as R administrator:
system(' echo "R_MAX_NUM_DLLS=150" >> /Library/Frameworks/R.framework/Resources/etc/Renviron')
For UBUNTU please modify the file
/usr/lib/R/etc/Renviron
and add
R_MAX_NUM_DLLS=150
in the end. Or you can run in R the
following command as R administrator:
system(' echo "R_MAX_NUM_DLLS=150" >> /usr/lib/R/etc/Renviron')
For other OS check https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html.
TCGAbiolinksGUI 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.
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/
This PDF shows how to install and execute the image using kitematic, which offers a graphical user interface (GUI) to control your app containers.
sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui
sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui
/home/$USER/docker
to the correct system path. Examples can
be found in this github
pagesudo docker stop tcgabiolinksgui
to stop itdocker run
and stopped).sudo docker start tcgabiolinksgui
The following commands should be used to start the graphical user interface.
library(TCGAbiolinksGUI)
TCGAbiolinksGUI()
To facilitate the use of this package, we have created some tutorial videos demonstrating the tool. Some sections have video tutorials that if clicked will redirect to the video on youtube. For the complete list of videos, please check this youtube list.
For each section we created some PDFs with detailing the steps of each section: Link to folder with PDFs
Please use Github issues if you want to file bug reports or feature requests.
Please cite both TCGAbiolinks package and TCGAbiolinksGUI:
Other related publications to this package:
If you used ELMER please cite:
If you used OncoPrint plot and Heatmap Plot please cite:
If you used maftools please also cite:
If you used Pathway plot please cite: