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Updated documentation. authored by Jean-Karim Heriche's avatar Jean-Karim Heriche
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Installation.md
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## Requirements
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.
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.
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.
From within an R console, install with:
```
> 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")
> 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")
```
and from Bioconductor: EBImage and RBioFormats
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* * *
## Launching the app
### Over the web
The IDE is accessible at https://shinyportal.embl.de (login required).
### From a command-line terminal
Open a terminal, download the code from the project's repository and run it from within the project directory:
```
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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
Alternatively, open the file image_data_explorer.R with RStudio then click the 'Run App' button.
### Using RStudio
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
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.
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)
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)
## Building and running the app in a container
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