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README.md

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Please refer to the [documentation][link-docs]. In particular, the
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- [API documentation][link-api]
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- [API documentation][link-api]
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and the tutorials:
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- [Paired integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/paired_integration_cite-seq.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/paired_integration_cite-seq.ipynb)
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- [Trimodal integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/trimodal_integration.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/trimodal_integration.ipynb)
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- [Paired integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/paired_integration_cite-seq.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/paired_integration_cite-seq.ipynb)
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- [Trimodal integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/trimodal_integration.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/trimodal_integration.ipynb)
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## Installation
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docs/contributing.md

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Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
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- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
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- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
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- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
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- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
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- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
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- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
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- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
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- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
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- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
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- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
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See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
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on how to write documentation.
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#### Hints
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- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
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if you do so can sphinx automatically create a link to the external documentation.
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- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
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the `nitpick_ignore` list in `docs/conf.py`
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- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
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if you do so can sphinx automatically create a link to the external documentation.
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- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
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the `nitpick_ignore` list in `docs/conf.py`
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#### Building the docs locally
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