Single-cell transcriptome querying tool
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.
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:
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
Check if the package can be imported in the Python interpreter:
import Cell_BLAST as cb print(cb.__version__)
Online documentation can be found here.
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
Feel free to submit an issue or contact us at firstname.lastname@example.org for problems about the Python package, website or database.
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