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Cyto aims to make available new computational cytometry tools to scientists with and without a bioinformatics background. Writing analysis pipelines using the workflow platform Anduril enables language-agnostic integration of new methods, Docker allows multi-OS compatibility, and Python libraries (flask and dash) allow user interaction.

Documentation

User guide with examples

Developer guide with examples

Quick start guide

Install Cyto in two steps

  1. Install Docker CE or Docker Desktop flavor for your operating system from https://www.docker.com/products/docker-desktop (for iOS and Windows) or your Linux repository. Note: It is a good practice to change the settings in Docker so that it can see enough resources from your computer (CPU, Memory, Storage, etc).
  2. In a Terminal or PowerShell type docker pull anduril/cyto to get the latest image available at Docker Hub

When new versions are available you can update it with docker pull anduril/cyto

Run Cyto

  1. Launch the cyto container from the terminal with the following command: docker run --rm -p 9999:9999 -p 8050:8050 -v cyto:/projects anduril/cyto
  2. Point your browser to localhost:9999

Cyto analyses in a nutshell

  1. Create a new project by giving it a meaningful name.

    A Cyto project is associated to a dataset, if you decide to repeat an analysis with all but one sample, or adding new ones, it is recommended to create a new project so that all previous analyses are saved.

  2. Upload your data.

    Either one single CSV file that contains a "Sample" column, or multiple CSV/FCS files where the filenames are the sample names.

  3. Tell Cyto what to do and save your settings with yet another meaningful name.

    Adjust your settings for each step of the analysis. Click Run. When the buttons become active again you know the analysis has finished.

  4. Browse your results and make meaningful knowledge from your data.

    View Results will take you to the Results Browser.

How to cite Cyto

If Cyto helps your research please consider citing our preprint DOI: https://doi.org/10.1101/2020.05.28.120527

Contributors

  • Julia Casado
  • Oskari Lehtonen
  • Ville Rantanen

Updated