https://github.com/bioinformaticsfmrp/tcgabiolinksgui
TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/
https://github.com/bioinformaticsfmrp/tcgabiolinksgui
bioconductor gdc gui integrative r tcga-data tcgabiolinks
Last synced: 13 days ago
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TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/
- Host: GitHub
- URL: https://github.com/bioinformaticsfmrp/tcgabiolinksgui
- Owner: BioinformaticsFMRP
- Created: 2015-02-25T18:02:36.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2021-08-02T16:49:14.000Z (almost 4 years ago)
- Last Synced: 2025-05-07T18:15:36.915Z (13 days ago)
- Topics: bioconductor, gdc, gui, integrative, r, tcga-data, tcgabiolinks
- Language: R
- Homepage: http://bioinformaticsfmrp.github.io/TCGAbiolinksGUI
- Size: 90.4 MB
- Stars: 35
- Watchers: 8
- Forks: 14
- Open Issues: 33
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Introduction
TCGAbiolinksGUI was created to help users without knowledge of programming to search, download and analyze
TCGA data. This package offers a graphical user interface to the R/Bioconductor packages [TCGAbiolinks]( http://bioconductor.org/packages/TCGAbiolinks/) and [ELMER](http://bioconductor.org/packages/ELMER/) packages.
Also, some other useful packages from Bioconductor, such as [ComplexHeatmap](http://bioconductor.org/packages/ComplexHeatmap/) package has been used for data visualization.
A running version of the GUI is found in [http://tcgabiolinks.fmrp.usp.br:3838/](http://tcgabiolinks.fmrp.usp.br:3838/)
## Installing TCGAbiolinksGUI
To install the package from [Bioconductor devel repository](http://bioconductor.org/packages/devel/bioc/html/TCGAbiolinksGUI.html), please, use the code below.
```R
# for the moment it must be devel version of Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinksGUI", dependencies = TRUE)
```
To install the package development version from Github, please, use the code below.
```R
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
deps <- c("devtools")
for(pkg in deps) if (!pkg %in% installed.packages()) BiocManager::install(pkg, dependencies = TRUE)
devtools::install_github("tiagochst/ELMER.data")
devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI.data",ref = "R_3.4")
devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI")
```
## Docker image
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/
### Setting up image using graphical user interface (GUI)
This [PDF](https://drive.google.com/open?id=0B0-8N2fjttG-QXp5LVlPQnVQejg)
shows how to install and execute the image using [kitematic](https://kitematic.com/), which
offers a graphical user interface (GUI) to control your app containers.
### Setting up image using command-line
- Download image: docker pull tiagochst/tcgabiolinksgui
- To run RStudio Server and shiny-server, but the data is not saved if container is stopped:
`sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui`
1. For more information how data can be saved please read [this wiki](https://github.com/rocker-org/rocker/wiki/How-to-save-data) and see command below
- To run RStudio Server, shiny-server and save the results in the host machine please use the code below:
`sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui`
1. In case rstudio is not accessible please check if the folder created (docker) has the right permission
2. If your system is windows or mac you will need to change `/home/$USER/docker`
to the correct system path. Examples can be found in this [github page](https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine)
- To stop the image:
1. Run `sudo docker stop tcgabiolinksgui` to stop it
- To start the image again (after the first time ran with `docker run` and stopped).
1. Run `sudo docker start tcgabiolinksgui`
### Accessing tools after the image is running:
- TCGAbiolinksGUI will be available at :3334/tcgabiolinksgui
- RStudio will be available at :3333 (***username: rstudio*** , ***password:rstudio***)
## Quick start
The following commands should be used in order to start the graphical user interface.
```R
library(TCGAbiolinksGUI)
TCGAbiolinksGUI()
```
## Video tutorials
To facilitate the use of this package, we have created some tutorial videos demonstrating the tool.
Please check this [youtube list](https://www.youtube.com/playlist?list=PLoDzAKMJh15m40f7OqOLAW0nJwkVStJIJ).
## PDF tutorials
For each section we created some PDFs with detailing the steps of each section:
[Link to folder with PDFs](https://drive.google.com/drive/folders/0B0-8N2fjttG-Q25ldVVmUTVOTk0?usp=sharing)
## Citation
Please cite both TCGAbiolinks package and TCGAbiolinksGUI:
* 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.
* TCGAbiolinksGUI: A Graphical User Interface to analyze TCGA data. Manuscript in preparation.
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.
If you have used OncoPrint plot and Heatmap Plot please cite:
* Gu, Zuguang, Roland Eils, and Matthias Schlesner. "Complex heatmaps reveal patterns and correlations in multidimensional genomic data." Bioinformatics (2016): btw313
If you have used Pathway plot please cite:
* Luo, Weijun, Brouwer and Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), pp. 1830-1831.
# Increasing loaded DLL
If you receive this error message: `maximal number of DLLs reached...`
You will need to increase the maximum number of DLL R can load. R_MAX_NUM_DLLS
In MACOS just modify the file `/Library/Frameworks/R.framework/Resources/etc/Renviron`
and add `R_MAX_NUM_DLLS=110` in the end.
For other OS check https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html.