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scRNA-Seq visualization tool

Project description

Interactive single cell visualization application.
  • Run on Google App Engine or your desktop
  • Scales to > 6 million cells on commodity hardware
  • Share datasets with collaborators
  • Interactively create and share cell annotations
  • Explore multiple features and embeddings simultaneously

Local Usage

  • Install using pip:

    pip install cirrocumulus
  • Launch via the command line:

    cirro launch <path to dataset>

Google Cloud Platform (GCP) Deployment Instructions

  • Clone the cirrocumulus repository:

    git clone
  • Change your current working directory to cirrocumulus:

    cd cirrocumulus
  • Install Node.js.

  • Install JavaScript dependencies:

    npm i
  • Build the client:

    npm run-script build
  • Create or use an existing GCP project

  • Create an OAuth client id

    • In Google Console, navigate to APIs and Services > OAuth consent screen. Set the OAuth consent screen application name and add <PROJECT> to the list of “Authorized domains”
    • Go to Credentials and click “Create Credentials > OAuth client ID”. Enter “Web application” for “Application Type” and https://<PROJECT> for “Authorized JavaScript origins”. Click “Create” to create the credentials.
    • Copy OAuth client id into cirrocumulus/cirro/config.json.
  • Create App Engine by navigating to App Engine > Dashboard. You may choose the region where your application is hosted. Select the Python 3 Standard Environment.

  • Install the Google Cloud SDK. Type gcloud init in your terminal if this is your first time using the Google Cloud SDK.

  • Deploy the application using the command below. Remember to replace <PROJECT> with your project ID.:

    gcloud app deploy app.yaml --project=<PROJECT>

    Your project is available at https://<PROJECT>

  • Go to https://<PROJECT> in your web browser and login.

    • By default, no one is allowed to add datasets to your application.
    • In Google Console, navigate to Data Store > Entities and click on your email address. Add the property importer of type boolean and set it to true.
    • Go back to https://<PROJECT> and start adding datasets.
  • Read more about App Engine, such as how you can limit spending.

Developer Instructions

  • Install JavaScript dependencies:

    npm i
  • Build the client:

    npm run-script build
  • Install Python module in editable mode:

    pip install -r requirements.txt -e .
  • Add http://localhost:5000 to your Web application Outh client ID authorized JavaScript origins at APIs and Services > Credentials

  • Download the App Engine service account JSON key from IAM & admin > Service accounts (DO NOT SHARE THIS!) and set the environment variable GOOGLE_APPLICATION_CREDENTIALS:

    export GOOGLE_APPLICATION_CREDENTIALS=“/home/user/Downloads/service-account-file.json”

Project details

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