{"id":27957982,"url":"https://github.com/bioinformaticsfmrp/tcgabiolinksgui","last_synced_at":"2025-09-01T00:34:25.775Z","repository":{"id":27837820,"uuid":"31327862","full_name":"BioinformaticsFMRP/TCGAbiolinksGUI","owner":"BioinformaticsFMRP","description":"TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/","archived":false,"fork":false,"pushed_at":"2021-08-02T16:49:14.000Z","size":94799,"stargazers_count":35,"open_issues_count":33,"forks_count":14,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-05-07T18:15:36.915Z","etag":null,"topics":["bioconductor","gdc","gui","integrative","r","tcga-data","tcgabiolinks"],"latest_commit_sha":null,"homepage":"http://bioinformaticsfmrp.github.io/TCGAbiolinksGUI","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioinformaticsFMRP.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-02-25T18:02:36.000Z","updated_at":"2024-09-11T17:42:53.000Z","dependencies_parsed_at":"2022-09-03T11:42:45.146Z","dependency_job_id":null,"html_url":"https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioinformaticsFMRP%2FTCGAbiolinksGUI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioinformaticsFMRP%2FTCGAbiolinksGUI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioinformaticsFMRP%2FTCGAbiolinksGUI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioinformaticsFMRP%2FTCGAbiolinksGUI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioinformaticsFMRP","download_url":"https://codeload.github.com/BioinformaticsFMRP/TCGAbiolinksGUI/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252931507,"owners_count":21827112,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","gdc","gui","integrative","r","tcga-data","tcgabiolinks"],"created_at":"2025-05-07T18:15:42.521Z","updated_at":"2025-05-07T18:15:43.129Z","avatar_url":"https://github.com/BioinformaticsFMRP.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"![](inst/app/www/logo_gray2.png)\n\n# Introduction\n\nTCGAbiolinksGUI was created to help users without knowledge of programming to search, download and analyze \nTCGA data. This package offers a graphical user interface to the R/Bioconductor packages [TCGAbiolinks]( \thttp://bioconductor.org/packages/TCGAbiolinks/)  and [ELMER](http://bioconductor.org/packages/ELMER/) packages.\nAlso, some other useful packages from Bioconductor, such as [ComplexHeatmap](http://bioconductor.org/packages/ComplexHeatmap/)  package  has been used for data visualization.\n\nA running version of the GUI is found in [http://tcgabiolinks.fmrp.usp.br:3838/](http://tcgabiolinks.fmrp.usp.br:3838/)\n\n## Installing TCGAbiolinksGUI\n\nTo install the package from [Bioconductor devel repository](http://bioconductor.org/packages/devel/bioc/html/TCGAbiolinksGUI.html), please, use the code below. \n\n```R\n# for the moment it must be devel version of Bioconductor\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"TCGAbiolinksGUI\", dependencies = TRUE)\n```\n\nTo install the package development version from Github, please, use the code below.\n```R\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\ndeps \u003c- c(\"devtools\")\nfor(pkg in deps)  if (!pkg %in% installed.packages()) BiocManager::install(pkg, dependencies = TRUE)\ndevtools::install_github(\"tiagochst/ELMER.data\")\ndevtools::install_github(\"BioinformaticsFMRP/TCGAbiolinksGUI.data\",ref = \"R_3.4\")\ndevtools::install_github(\"BioinformaticsFMRP/TCGAbiolinksGUI\")\n```\n\n## Docker image\n\nTCGAbiolinksGUI is available as Docker image (self-contained environments that contain everything needed to run the software), \nwhich can be easily run on Mac OS, Windows and Linux systems. \n\nThe image can be obtained from Docker Hub: https://hub.docker.com/r/tiagochst/tcgabiolinksgui/\n\nFor more information please check: https://docs.docker.com/ and https://www.bioconductor.org/help/docker/\n\n### Setting up image using graphical user interface (GUI) \n\nThis [PDF](https://drive.google.com/open?id=0B0-8N2fjttG-QXp5LVlPQnVQejg) \nshows how to install and execute the image using [kitematic](https://kitematic.com/), which\noffers a  graphical user interface (GUI) to control your app containers.\n\n### Setting up image using command-line \n\n- Download image: docker pull tiagochst/tcgabiolinksgui\n- To run RStudio Server and shiny-server, but the data is not saved if container is stopped: \n`sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui`\n1. For more information how data can be saved please read [this wiki](https://github.com/rocker-org/rocker/wiki/How-to-save-data) and see command below \n\n- To run RStudio Server, shiny-server and save the results in the host machine please use the code below: \n`sudo docker run --name tcgabiolinksgui -d -P -v /home/$USER/docker:/home/rstudio -p 3333:8787 -p 3334:3838 tiagochst/tcgabiolinksgui`\n 1. In case rstudio is not accessible please check if the folder created (docker) has the right permission\n 2. If your system is windows or mac you will need to change  `/home/$USER/docker` \n 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)\n\n- To stop the image:\n1. Run  `sudo docker stop tcgabiolinksgui` to stop it\n\n- To start the image again (after the first time ran with `docker run` and stopped).\n1. Run  `sudo docker start tcgabiolinksgui` \n\n### Accessing tools after the image is running:\n\n- TCGAbiolinksGUI will be available at \u003cyour local IP\u003e:3334/tcgabiolinksgui\n- RStudio will be available at \u003cyour local IP\u003e:3333 (***username: rstudio*** , ***password:rstudio***)\n\n## Quick start\n\nThe following commands should be used in order to start the graphical user interface.\n\n```R\nlibrary(TCGAbiolinksGUI)\nTCGAbiolinksGUI()\n```\n## Video tutorials\n\nTo facilitate the use of this package, we have created some tutorial videos demonstrating the tool.\nPlease check this [youtube list](https://www.youtube.com/playlist?list=PLoDzAKMJh15m40f7OqOLAW0nJwkVStJIJ).\n\n## PDF tutorials\n\nFor each section we created some PDFs with detailing the steps of each section: \n[Link to folder with PDFs](https://drive.google.com/drive/folders/0B0-8N2fjttG-Q25ldVVmUTVOTk0?usp=sharing)\n\n\n## Citation\n\nPlease cite both TCGAbiolinks package and TCGAbiolinksGUI: \n\n* 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.\n\n* TCGAbiolinksGUI: A Graphical User Interface to analyze TCGA data. Manuscript in preparation.\n\nAlso, if you have used ELMER analysis please cite:\n\n* Yao, L., Shen, H., Laird, P. W., Farnham, P. J., \u0026 Berman, B. P. \"Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.\" Genome Biol 16 (2015): 105.\n* 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.\n\n\nIf you have used  OncoPrint plot and Heatmap Plot please cite:\n\n* Gu, Zuguang, Roland Eils, and Matthias Schlesner. \"Complex heatmaps reveal patterns and correlations in multidimensional genomic data.\" Bioinformatics (2016): btw313\n\nIf you have used  Pathway plot please cite:\n\n* Luo, Weijun, Brouwer and Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), pp. 1830-1831.\n\n# Increasing loaded DLL\n\nIf you receive this error message:  `maximal number of DLLs reached...`\nYou will need to increase the maximum number of DLL R can load.  R_MAX_NUM_DLLS\nIn MACOS just modify the file `/Library/Frameworks/R.framework/Resources/etc/Renviron`\nand add `R_MAX_NUM_DLLS=110` in the end.\n\nFor other OS check https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinformaticsfmrp%2Ftcgabiolinksgui","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioinformaticsfmrp%2Ftcgabiolinksgui","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinformaticsfmrp%2Ftcgabiolinksgui/lists"}