cellmapper 0.1.1

k-NN-based mapping of cells across representations

CellMapper

k-NN-based mapping of cells across representations to tranfer labels, embeddings and expression values. Works for millions of cells, on CPU and GPU, across molecular modalities, between spatial and non-spatial data, for arbitrary query and reference datasets. Using faiss to compute k-NN graphs, CellMapper takes about 30 seconds to transfer cell type labels from 1.5M cells to 1.5M cells on a single RTX 4090 with 60 GB CPU memory.

Getting started

Please refer to the [documentation][], in particular, the API documentation.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing uv.

There are several alternative options to install cellmapper:

1. Install the latest development version:

pip install git+https://github.com/quadbio/cellmapper.git@main

Release notes

See the changelog.

Contact

If you found a bug, please use the issue tracker.

Citation

Please cite this GitHub repo if you find CellMapper useful for your research.