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Update the README with link and badge to the docs
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README.md

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[![Coverage][badge-coverage]][coverage]
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[![Pre-commit.ci][badge-pre-commit]][pre-commit]
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[![PyPI][badge-pypi]][pypi]
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[![Documentation][badge-docs]][docs]
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[badge-tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml/badge.svg
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[badge-coverage]: https://codecov.io/gh/quadbio/cellmapper/branch/main/graph/badge.svg
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[badge-pre-commit]: https://results.pre-commit.ci/badge/github/quadbio/cellmapper/main.svg
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[badge-pypi]: https://img.shields.io/pypi/v/cellmapper.svg
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[badge-docs]: https://img.shields.io/readthedocs/cellmapper
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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.
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Inspired by scanpy's [ingest][] and the [HNOCA-tools][] packages.
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Inspired by scanpy's [ingest][] and the [HNOCA-tools][] packages. Check out the [docs][] to learn more.
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## Installation
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This will transfer data from the reference to the query dataset, including celltype labels stored in ``ref.obs``, a UMAP embedding stored in ``ref.obsm``, and expression values stored in ``ref.X``.
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There are many ways to customize this, e.g. use different ways to compute k-NN graphs and to turn them into mapping matrices, and we implement a few methods to evaluate whether your k-NN transfer was sucessful.
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There are many ways to customize this, e.g. use different ways to compute k-NN graphs and to turn them into mapping matrices, and we implement a few methods to evaluate whether your k-NN transfer was sucessful. Check out the [docs][] to learn more.
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## Release notes
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[issue tracker]: https://github.com/quadbio/cellmapper/issues
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[tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml
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[changelog]: https://cellmapper.readthedocs.io/en/latest/changelog.html
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[api documentation]: https://cellmapper.readthedocs.io/en/latest/api.html
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[docs]: https://cellmapper.readthedocs.io/
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[pypi]: https://pypi.org/project/cellmapper
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[coverage]: https://codecov.io/gh/quadbio/cellmapper
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[pre-commit]: https://results.pre-commit.ci/latest/github/quadbio/cellmapper/main

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