OligoR is a native HDX/MS data processing application dedicated to oligonucleotides and their complexes. OligoR accepts open-format MS files, and can be used for data processing and the generation of publication-quality figures for HDX/MS, MS kinetics, and MS titrations experiments.
Although developed with oligonucleotides in mind, OligoR can be used for other types of analytes.
OligoR is an entirely open-source application, that can be run from the source code in R, or more simply from a Docker container.
OligoR may be accessed online at oligor.seis.me. The server may not always be running. Feel free to contact me if that is the case.
Download or clone the source code to your local machine. All dependencies will be installed on the first use of the app, which will take some time.
Create a project at the root of the OligoR directory, or set the working directory to this location using the following command (where
PATH_TO_OLIGOR with the actual path to OligoR on your machine):
To update, either download the latest version of OligoR, or if you have cloned the repository simply pull the changes.
This method requires the installation of Docker Desktop.
From a terminal, execute either of the following command to obtain the OligoR image.
docker pull ghcr.io/ericlarg4/oligor:master
docker pull ericlarg4/oligor:master
To update, simply use the above command again, or click on pull in the Docker desktop software (click on the three dot menu on the image line, then click on pull). This image is automatically re-built when the source code is changed.
To open the app, either:
shiny::runApp(appDir = 'app'), assuming you work in a project and/or have set the working directory to OligoR as described above
shiny::runApp(appDir = 'PATH_TO_OLIGOR/OligoR/app')if you have not set the working directory or created a project for OligoR
To open the app with Docker, either:
Use Docker Desktop GUI:
Open Docker Desktop
In the Images panel, hover the cursor over ghcr.io/ericlarg4/oligor, then click on Run
In the Optional settings, set the first Host port to 3838
Click on Run
In the Containers panel, which should now be opened, click on the Open with browser icon (immediatly to the right of the Started time, on the right-hand side of the line)
After using OligoR, you may stop and remove the container (using the dedicated icons), or keep it running for further uses
Use a terminal:
docker run --rm -p 3838:3838 ghcr.io/ericlarg4/oligor:master
docker ps -q --filter ancestor=ghcr.io/ericlarg4/oligor:master | xargs docker stopin a terminal
Refer to the Wiki of the repository.
Demo data files are available in the demo data directory of OligoR, including both raw and processed data.