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
Visualize 3-d embeddings
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 https://github.com/klarman-cell-observatory/cirrocumulus
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>.appspot.com 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>.appspot.com 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>.appspot.com.
Go to https://<PROJECT>.appspot.com 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>.appspot.com 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”
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