Cell-BLAST 0.1.2

Single-cell transcriptome querying tool

Cell BLAST

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 preprint 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=3.6 && source activate cb

Now follow the instructions below to install Cell BLAST:

1. Make sure you have a working version of tensorflow or tensorflow-gpu (version >= 1.5). You can follow the official instructions about how to install tensorflow (and dependencies like CUDA and CuDNN for the GPU version), or just install via anaconda, which handles dependencies automatically:

   For installing the GPU supported version: conda install tensorflow-gpu=1.8

   For installing the CPU only version: conda install tensorflow=1.8

2. Install Cell BLAST by running: pip install Cell-BLAST

3. Check if the package can be imported in 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.

Repository structure

• The Cell_BLAST directory contains the Cell BLAST python package.
• The Datasets directory contains scripts used for building the ACA database.
• The Evaluation directory contains scripts used for benchmarking and producing some figures of the manuscript.
• The doc directory contains files used to generate the online documentation.
• The test directory contains unit tests for the python package.

Contact

Feel free to submit an issue or contact us at [e-mail] for problems about the python package, website or database.