CellO is a tool for classifying single-cell RNA-seq data against the graph-structured Cell Ontology. Each cell type in the Cell Ontology is associated with a binary classifier for classifying cells for the given cell type. These binary classifiers are linear models and thus, each gene's coefficient provides a description of the gene's importance for classifying the given cell type. The CellO Viewer is a web application for exploring these gene-wise model coefficients across the Cell Ontology. Each model's largest coefficients can be interpreted as a cell type-specific expression signature.
For more details, see the manuscript: Bernstein, M.N., Ma, J., Gleicher, M., Dewey, C.N. (2020).CellO: Comprehensive and hierarchical cell type classification of human cellswith the Cell Ontology. bioRxiv
The tool runs online at https://uwgraphics.github.io/CellOViewer/
cd client
npm install
Note: all the frontend files are in the client folder, make sure you go into the client folder by cd client before doing anything npm related.
To run a local server for testing the website, run the following command:
npm run serve
To deploy the website, run the following commands:
cd client
npm run build
bash deploy.sh
The np run build command will compile the website. Github Pages requires that the website's files be located in the docs directory. The command bash deploy.sh copies the relevant files from client/dist (i.e. the location where the compiled files are written to by npm) to docs. Once the docs directory stores the latest version of the website, pushing the code to Github will trigger Github Pages to serve the new website.
npm run lint
CellO Viewer is BSD 3-clause licensed.