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Single-cell transcriptome querying tool

Project description


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Cell BLAST is a cell querying tool for single-cell transcriptomics data.

For each query cell, it searches for most similar cells in the reference database. Annotations in reference cells, e.g. cell type, can then be transfered to query cells based on cell-to-cell similarities. See our publication for details.

Installing the Python package

We only support installation via pip right now.

Installation within virtual environments are recommended, see virtualenv or conda.

For conda, here's a one-liner to set up an empty environment for installing Cell BLAST:

conda create -n cb python=3.9 && conda activate cb

Then follow the instructions below to install Cell BLAST:

  1. Install Cell BLAST from PyPI by running:

    pip install Cell-BLAST

    Or, install an editable dev version by running the following command under the root directory of this repo:

    flit install -s

  2. Check if the package can be imported in the Python interpreter:

    import Cell_BLAST as cb


Online documentation can be found here.

Web-based interface

We also provide a Web-based service for off-the-shelf querying of our ACA reference panels.

Reproduce results in the paper

To reproduce results, please check out the rep branch.


Feel free to submit an issue or contact us at for problems about the Python package, website or database.

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