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UCSCXenaShiny \u003cimg src=\"https://raw.githubusercontent.com/openbiox/wiki/master/static/img/logo-long.png\" align=\"right\" width=\"200\"/\u003e\n\n[![CRAN\nstatus](https://www.r-pkg.org/badges/version/UCSCXenaShiny)](https://cran.r-project.org/package=UCSCXenaShiny)\n[![](https://cranlogs.r-pkg.org/badges/grand-total/UCSCXenaShiny?color=orange)](https://cran.r-project.org/package=UCSCXenaShiny)\n[![lifecycle](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) \n![R-CMD-check](https://github.com/openbiox/UCSCXenaShiny/workflows/R-CMD-check/badge.svg)\n[![check in Biotreasury](https://img.shields.io/badge/Biotreasury-collected-brightgreen)](https://biotreasury.rjmart.cn/#/tool?id=61144)\n\n![](https://ucscxenashiny-1301043367.cos.ap-shanghai.myqcloud.com/Shiny-figures/Github_readme.png)\n\n**UCSCXenaShiny** is an R package for interactively exploring UCSC Xena.\nIt is mainly designed to provide a web app (built on the top of [`{shiny}`](https://shiny.posit.co/) framework and [`{UCSCXenaTools}`](https://github.com/ropensci/UCSCXenaTools/) package) for downloading,\nanalyzing and visualizing datasets from [UCSC\nXena](https://xenabrowser.net/datapages/).\n\n\n\n![Alt](https://repobeats.axiom.co/api/embed/2f1f0c9a7a5c3c710febb3ee3d1e26f249d5a3ed.svg \"Repobeats analytics image\")\n\nPlease cite any of the following articles when you used **UCSCXenaShiny** in your study:\n\n---------------\n\n**V2**\n\n- Shensuo Li, Yuzhong Peng, Minjun Chen, Yankun Zhao, Yi Xiong, Jianfeng Li, Peng Luo, Haitao Wang, Fei Zhao, Qi Zhao, Yanru Cui, Sujun Chen, Jian-Guo Zhou, Shixiang Wang,  Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny, Communications Biology, 1200 (2024),  https://doi.org/10.1038/s42003-024-06891-2\n\n\n**V1**\n\n- Shixiang Wang\u003csup\u003e\\#\u003c/sup\u003e, Yi Xiong\u003csup\u003e\\#\u003c/sup\u003e, Longfei Zhao\u003csup\u003e\\#\u003c/sup\u003e, Kai Gu\u003csup\u003e\\#\u003c/sup\u003e, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data, Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561.\n\n---------------\n\n## :cloud: Use on cloud\n\nIf you don't want to install R and packages locally, or you have no programming experience, try using this tool on `Oncoharmony Network` (`http://shiny.zhoulab.ac.cn/UCSCXenaShiny`) or `Hiplot ORG` platform (`https://shiny.hiplot.cn/ucsc-xena-shiny`).\n\nWe have deployed two additional apps: a basic version of V2 (`https://shiny.zhoulab.ac.cn/UCSCXenaShiny_basic/`) and an archive version of V1 (`https://shiny.zhoulab.ac.cn/UCSCXenaShinyV1/`, code please see v1 branch).\n\n## :snake: Use with Conda\n\n| Name | Downloads | Version | Platforms |\n| --- | --- | --- | --- |\n| [![Conda Recipe](https://img.shields.io/badge/recipe-r--ucscxenashiny-green.svg)](https://github.com/conda-forge/r-ucscxenashiny-feedstock) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/r-ucscxenashiny.svg)](https://github.com/conda-forge/r-ucscxenashiny-feedstock) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/r-ucscxenashiny.svg)](https://github.com/conda-forge/r-ucscxenashiny-feedstock) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/r-ucscxenashiny.svg)](https://github.com/conda-forge/r-ucscxenashiny-feedstock) |\n\nInstall from `conda-forge` channel with:\n\n```bash\nconda install -c conda-forge r-ucscxenashiny\n```\n\nIt is possible to list all of the versions of `r-ucscxenashiny` available on your platform with:\n\n```bash\nconda search r-ucscxenashiny --channel conda-forge\n```\n\n## :package: Use with Docker\n\n\u003cimg alt=\"Docker Image Version (latest by date)\" src=\"https://img.shields.io/docker/v/shixiangwang/ucscxenashiny?color=blue\"\u003e\n\u003cimg alt=\"Docker Image Size (latest by date)\" src=\"https://img.shields.io/docker/image-size/shixiangwang/ucscxenashiny\"\u003e\n\u003cimg alt=\"Docker Pulls\" src=\"https://img.shields.io/docker/pulls/shixiangwang/ucscxenashiny\"\u003e\n\nUCSCXenaShiny has corresponding docker image at \u003chttps://hub.docker.com/r/shixiangwang/ucscxenashiny/\u003e, you can install the latest version with:\n\n```bash\ndocker pull shixiangwang/ucscxenashiny\n```\n\u003e From v2, docker pull from GitHub `ghcr.io` registry is also supported, e.g., `docker pull ghcr.io/openbiox/ucscxenashiny:master`.\n\nAll versions can be found at \u003chttps://hub.docker.com/r/shixiangwang/ucscxenashiny/tags/\u003e.\nTo use a specified version (e.g., `2.0.0`; latest code commit will auto-build a tag `master`), run the following command to install:\n\n```bash\ndocker pull shixiangwang/ucscxenashiny:2.0.0\n# docker pull shixiangwang/ucscxenashiny:master  # For latest code, unstable\n```\n\nRun the latest stable docker image and keep it at background with:\n\n```bash\ndocker run -d --name xenashiny -p 3838:3838 shixiangwang/ucscxenashiny\n```\n\nNow you should find the Shiny when you open URL `http://127.0.0.1:3838` with your web browser.\nIf you deploy the docker in a public (cloud) Linux server, change `127.0.0.1` to the host IP.\n\n\u003e For the first time, it may return a failure about 'take a long time to respond', please\n\u003e refresh the web page.\n\nIf the application failed to start. Check if the container has installed all dependencies.\n\n```bash\ndocker exec xenashiny R -e 'source(system.file(\"shinyapp/utils_pkgs.R\", package = \"UCSCXenaShiny\"))'\n```\n\nOr you can interactively check the container:\n\n```bash\ndocker exec -it xenashiny /bin/bash\n```\n\nYou can manage the deployed container with the following commands:\n\n```bash\n# Stop the container\ndocker stop xenashiny\n# Start the container\ndocker start xenashiny\n```\n\n## :arrow_double_down: Manual installation\n\nYou can install stable release of **UCSCXenaShiny** from CRAN with:\n\n```r\ninstall.packages(\"UCSCXenaShiny\")\n```\n\nYou can install the development version of **UCSCXenaShiny** from Github\nwith:\n\n```r\nremotes::install_github(\"openbiox/UCSCXenaShiny\")\n```\n\nOr r-universe:\n\n```r\ninstall.packages(\"UCSCXenaShiny\", repos = c(\"https://openbiox.r-universe.dev\", \"https://cran.r-project.org\"))\n```\n\nOther dependent R packages specific to the Shiny application will be automatically installed when you start with `app_run()` command. If you failed to install **UCSCXenaShiny**, please check if the following system dependencies have been properly installed or see [**Troubleshooting**](#hammer_and_wrench-troubleshooting) section for specific installation issues.\n\n### System dependencies installation\n\nWhen you use Windows/MacOS, please skip reading this sub-section.\n\nAs Linux distributions are very diverse,  here we only test the installation of **UCSCXenaShiny** on common used Ubuntu/CentOS. If you are using other Linux distributions, you need to solve the system dependencies installation problems yourself when you encounter R package installation errors. However, the installation of system dependencies on Ubuntu/CentOS could be very good references.\n\n\u003e Please note all commands below are execuated with `root`.\n\n**Ubuntu**:\n\n```bash\napt update -y \u0026\u0026 apt install -y libcurl4-openssl-dev libssl-dev libxml2-dev \\\n\tlibgmp3-dev libmpfr-dev\n```\n\n**CentOS**:\n\n```bash\nyum update -y \u0026\u0026 yum install -y libcurl-devel openssl-devel libxml2-devel \\\n\tgmp-devel mpfr-devel libjpeg-devel cairo-devel\n```\n\n\n\n## :beginner: Usage\n\nFirst load package:\n\n```r\nlibrary(UCSCXenaShiny)\n```\n\nStart Shiny in your R console (ignore this if you just want to use functions in this package):\n\n```r\napp_run()\n# At default, the Shiny is running under client mode\n# It means the data queried from remote UCSC Xena server will\n# be saved to temporary directory determined by R\n# If you frequently use this tool or deploy this tool as a web service for multiple users\n# It is recommended to run it with 'server' mode\n# i.e.,\n#\n# app_run(\"server\")\n```\n\nIf you want deploy UCSC Xena Shiny with Shiny Server, please copy `App.R` and `www/` directory under [`shinyapp`](https://github.com/openbiox/UCSCXenaShiny/tree/master/inst/shinyapp).\n`xena.runMode` on the top of `App.R` is recommended to set as `\"server\"` instead of `\"client\"` (default).\n\nFor advanced users, examples for illustrating useful functions to obtain and analyze data are described in vignette.\n\nAll exported data and functions are organized at [here](https://openbiox.github.io/UCSCXenaShiny/reference/index.html).\n\n`xena.cacheDir` and `xena.zenodoDir` are two options to control where to store data.\n\ne.g.,\n\n```r\nxena.cacheDir = \"/xena\"\nxena.zenodoDir = \"/xena/datasets\"\n\noptions(xena.cacheDir = xena.cacheDir, xena.zenodoDir = xena.zenodoDir)\n\noptions(xena.runMode = \"server\")\n```\n\nOption `xena.runMode` can be used to control the way how the Shiny works.\nIt can be 'client' or 'server'. You can directly set it in `app_run()`.\n\n## :movie_camera: Videos\n\n#### UCSCXenaShiny v2\n**Chinese website**\n- Home page: \u003chttps://www.bilibili.com/video/BV1rT421k7Zv\u003e\n- T•P•C Modules: \u003chttps://www.bilibili.com/video/BV1E14218779\u003e \n- T•P•C Pipelines: \u003chttps://www.bilibili.com/video/BV141421t71g\u003e\n- Repository/General Analysis/Download: \u003chttps://www.bilibili.com/video/BV1TZ421K7VH\u003e\n\n**English website**: \u003chttps://www.youtube.com/watch?v=VnIlzcVB1Ow\u0026list=PLN1jxcOQONG6pH8zvHr-qhI3MMtvluITf\u003e\n\n#### UCSCXenaShiny v1\n\n- Home page: \u003chttps://www.bilibili.com/video/bv1R84y1F7WT\u003e.\n- Repository page: \u003chttps://www.bilibili.com/video/bv1Mq4y1J73o\u003e.\n- General Analysis page: \u003chttps://www.bilibili.com/video/bv1p64y1U7iU\u003e.\n- Quick PanCan Analysis page: \u003chttps://www.bilibili.com/video/bv1o64y1y7jW\u003e.\n- Features:\n  - Genomic Signature: \u003chttps://www.bilibili.com/video/bv1zB4y1c7eB\u003e.\n  - Upload custom data for general analysis: \u003chttps://www.bilibili.com/video/BV1pf4y1j7eP\u003e.\n  Please note that upload files must in the format of csv/tsv (gz compression is supported) and\n  files must have extension tsv/txt/csv/gz.\n\n## :hammer_and_wrench: Troubleshooting\n\n1. `ERROR: dependencies ‘gmp’, ‘Rmpfr’ are not available for package ‘PMCMRplus’` or `ERROR: dependency ‘pairwiseComparisons’ is not available for package ‘ggstatsplot’`.\n\n   **Your operating system lacks `gmp` and `Rmpfr` development libraries.**\n   \n   ```bash\n   # Ubuntu\n   apt install -y libgmp3-dev libmpfr-dev\n   # CentOS\n   yum install -y gmp-devel mpfr-devel\n   ```\n   \n2. `installation of package ‘gridtext’ had non-zero exit status` with error info `grid-renderer.h:61:94: error: no matching function for call to ‘Rcpp::Vector\u003c10, Rcpp::PreserveStorage\u003e::Vector(int, bool\u0026, const GraphicsContext\u0026)’`.\n   \n    **You have an older C++ version which cannot support C++11 features. This error seems only happen on CentOS. Install a newer C++ and set it as default compiler for R would fix this problem.** \n    \n    ```bash\n    yum install centos-release-scl\n    yum install devtoolset-9\n    # If you use your non-root account to install packages, \n    # change /root to /home/your_id in the following command\n    mkdir -p /root/.R\n    vi /root/.R/Makevars \n    ```\n    \n     **Append content to the openning file.**\n\n    ```bash\n    CXX11=/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11\n    ```\n\n\n3. `installation of package ‘nloptr’ had non-zero exit status` with error info `libtool: link: ERROR: no information for variable 'AR' cru`.\n\n   **The latest version of `nloptr` can only support R\u003e=4.0. When you are using R3.6 or below would have this issue. So install an older version in R console can fix this.**\n\n   ```R\n   packageurl \u003c- \"https://cran.r-project.org/src/contrib/Archive/nloptr/nloptr_1.2.1.tar.gz\"\n   \n   install.packages(packageurl, repos=NULL, type=\"source\")\n   ```\n\n   \u003e Reference: https://stackoverflow.com/questions/62900525/install-lme4-from-cran-on-ubuntu\n\n4. `package ‘pacman’ is not available` or similar.\n\n   **Install it by hand in R console.**\n\n   ```R\n   install.packages(\"pacman\")\n   ```\n\n5. `there is no package called ‘shinythemes’` or similar.\n\n   **Install it by hand in R cosole.**\n\n   ```R\n   install.packages(\"shinythemes\")\n   ```\n\n6. Install package `gganatogram` failed or similar.\n\n   **Install it by hand in R cosole.**\n\n   ```R\n   if (!requireNamespace(\"gganatogram\")) {\n      library(remotes)\n      tryCatch(\n         remotes::install_github(\"jespermaag/gganatogram\"),\n         error = function(e) {\n            remotes::install_git(\"https://gitee.com/XenaShiny/gganatogram\")\n         }\n      )\n   }\n   ```\n\n7. Install package `ggradar` failed or similar.\n\n   **Install it by hand in R cosole.**\n\n   ```R\n   if (!requireNamespace(\"ggradar\")) {\n      library(remotes)\n      tryCatch(\n         remotes::install_github(\"ricardo-bion/ggradar\"),\n         error = function(e) {\n            remotes::install_git(\"https://gitee.com/XenaShiny/ggradar\")\n         }\n      )\n   }\n   ```\n\n\n## :writing_hand: Author\n\n  - [Shixiang Wang](https://github.com/ShixiangWang)\n  - [Yi Xiong](https://github.com/Byronxy)\n  - [Shensuo Li](https://github.com/lishensuo)\n  - [Longfei Zhao](https://github.com/longfei8533)\n  - [Kai Gu](https://github.com/kaigu1990)\n  - [Yuzhong Peng](https://github.com/mugpeng)\n  - [Yin Li](https://github.com/yinlisssss)\n  - [Fei Zhao](https://github.com/fei0810)\n\n## :page_with_curl: LICENSE\n\nGPLv3 © [Openbiox](https://github.com/openbiox)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenbiox%2FUCSCXenaShiny","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenbiox%2FUCSCXenaShiny","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenbiox%2FUCSCXenaShiny/lists"}