Remote access via Caltech PEL


This application is hosted for public use by the Proteome Exploration Laboratory at the Beckman Institute at Caltech:

Launch application

You may also run the application locally by following the instructions below.

Local installation with Docker


The application is available as a Docker image on Docker Hub. To use the application locally, follow these instructions:

  1. Clone this repository to a local directory using

    $ git clone https://github.com/ejmackrell/tidyproteomics-interactive <dir>

  2. Download, install, and start Docker Desktop

  3. Navigate to the directory and run the command

    $ docker compose up

    to pull the Docker image, build a Docker container, and run the application.

You may access the running application at http://localhost:3838. To change the port from the default 3838, edit the specification for ports in docker-compose.yml (e.g., to 5000:3838 for accessing the application at port 5000).

Local installation with RStudio


You can also run and modify the application in RStudio by following the instructions below.

Cloning the repository in RStudio

  1. Install {renv} (if it is not installed already) by executing

    install.packages("renv")

    in the R console.

  2. Create a new version-controlled project in RStudio and provide the URL for this repository.

Restoring the project

  1. Once the project is opened in your RStudio session, run the command

     renv::activate()

    to load the project environment, which should download the appropriate version of {BiocManager}.

  2. Restore the project with the command

    renv::restore()

    to install all of the packages required for the project. If the repository for a Bioconductor package is not identified, you can manually install these packages individually by executing

    renv::install("bioc::{package name}")

    or instead as a group by specifying Bioconductor repositories with

    renv::restore(repos = BiocManager::repositories())