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## Requirements
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The IDE needs a computer with an [R environment version >=3.5.0](https://www.r-project.org/). The IDE requires some R packages and will try to install them if it can't detect them on the system. In case of problems, it may be better to install the required packages manually.
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The IDE requires the following packages from CRAN: devtools, data.table, DT, shiny, shinyFiles, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, shinybusy, assertthat, ggplot2, plotly, RANN, MASS, dbscan, uwot, xgboost, Ckmeans.1d.dp, e1071, caret, RColorBrewer.
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The IDE requires the following packages from CRAN: devtools, data.table, DT, shiny, shinyFiles, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, shinybusy, assertthat, ggplot2, plotly, RANN, MASS, dbscan, uwot, xgboost, Ckmeans.1d.dp, e1071, caret, RColorBrewer, aws.s3.
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From within an R console, install with:
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```
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> install.packages("devtools", "data.table", "DT", "shiny", "shinyFiles", "shinycssloaders", "shinydashboard", "shinyjs", "shinyWidgets", "shinybusy", "assertthat", "ggplot2", "plotly", "RANN", "MASS", "dbscan", "uwot", "xgboost", "Ckmeans.1d.dp", "e1071", "caret", "RColorBrewer")
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> install.packages("devtools", "data.table", "DT", "shiny", "shinyFiles", "shinycssloaders", "shinydashboard", "shinyjs", "shinyWidgets", "shinybusy", "assertthat", "ggplot2", "plotly", "RANN", "MASS", "dbscan", "uwot", "xgboost", "Ckmeans.1d.dp", "e1071", "caret", "RColorBrewer", "aws.s3")
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```
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and from Bioconductor: EBImage and RBioFormats
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* * *
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## Launching the app
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### Over the web
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The IDE is accessible at https://shinyportal.embl.de (login required).
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### From a command-line terminal
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Open a terminal, download the code from the project's repository and run it from within the project directory:
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```
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> R -e 'shiny::runApp("image_data_explorer.R", host = "0.0.0.0", port = 5476)'
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```
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The app is then accessible from a web browser (on the same machine the app was started on) at http://127.0.0.1:5476
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The app is then accessible from a web browser (on the same machine the app was started on) at http://127.0.0.1:5476
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### Using RStudio
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Alternatively, open the file image_data_explorer.R with RStudio then click the 'Run App' button.
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Alternatively, download the project's directory as a zip archive ([latest version](https://git.embl.de/heriche/image-data-explorer/-/archive/master/image-data-explorer-master.zip)) and unpack the archive. Start RStudio, navigate to the project's directory and open the file image_data_explorer.R then click the 'Run App' button. The app is accessible from a web browser (on the same machine RStudio is running on) at http://127.0.0.1:5476
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Before using the app, check that the data conforms to the structure laid out in [Preparing the data for use with the IDE](./Preparing the data for use with the IDE) page.
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If you're experiencing problems, please check the [known issues and troubleshooting](./Known issues and troubleshooting) page before [submitting a new issue](https://git.embl.de/meechan/image-data-explorer/-/issues)
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If you're experiencing problems, please check the [known issues and troubleshooting](./Known issues and troubleshooting) page before [submitting a new issue](https://git.embl.de/heriche/image-data-explorer/-/issues)
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## Building and running the app in a container
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... | ... | |