{"repo":"quadbio/cellmapper","free":true,"listed":false,"github":"https://github.com/quadbio/cellmapper","clone":"git clone https://github.com/quadbio/cellmapper.git","description":"k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.","language":"Python","stars":16,"topics":["data-integration","genomics","k-nn","representation-learning","scrna-seq","single-cell","spatial-biology"],"license":"MIT","category":"data-pipelines","readme_excerpt":"CellMapper [![Tests][badge-tests]][tests] [![Coverage][badge-coverage]][coverage] [![Pre-commit.ci][badge-pre-commit]][pre-commit] [![PyPI][badge-pypi]][pypi] [![Documentation][badge-docs]][docs] [![Downloads][badge-downloads]][downloads] [![Zenodo][badge-zenodo]][zenodo] [badge-tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml/badge.svg [badge-coverage]: https://codecov.io/gh/quadbio/cellmapper/branch/main/graph/badge.svg [badge-pre-commit]: https://results.pre-commit.ci/badge/github/quadbio/cellmapper/main.svg [badge-pypi]: https://img.shields.io/pypi/v/cellmapper.svg [badge-docs]: https://img.shields.io/readthedocs/cellmapper [badge-downloads]: https://static.pepy.tech/badge/cellmapper [badge-zenodo]: https://zenodo.org/badge/973714072.svg k-NN-based mapping of cells across representations to transfer 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. Inspired by previous tools, including scanpy's [ingest][] and the [HNOCA-tools][] packages. Check out the 📚 [docs][] to learn more, in particular our [tutorials][]. ✨ Key use cases - 🧬 Transfer cell type labels and expression values from dissociated to spatial datasets. - ↔️ Transfe","default_branch":null,"files":null,"tree":[],"storefront":"/r/quadbio","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/quadbio/cellmapper/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}