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update docs
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cailigd committed Dec 7, 2022
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## 1. Introduction <a name="Introduction"></a>
Germline mutation rates are crucial parameters in genetics, genomics and evolutionary biology. It is long known that mutation rates vary substantially across the genome, but existing methods can only obtain very rough estimates of local mutation rates and are difficult to be applied to non-model species.
Germline mutation rates are important in genetics, genomics and evolutionary biology. It is long known that mutation rates vary substantially across the genome, but existing methods can only obtain very rough estimates of local mutation rates and are difficult to be applied to non-model species.

**MuRaL**, short for **Mu**tation **Ra**te **L**earner, is a generalizable framework to estimate single-nucleotide mutation rates based on deep learning. MuRaL has better predictive performance at different scales than current state-of-the-art methods. Moreover, it can generate genome-wide mutation rate maps with rare variants from a moderate number of sequenced individuals (e.g. ~100 individuals), and can leverage transfer learning to further reduce data and time requirements. It can be applied to many sequenced species with population polymorphism data.

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6 changes: 3 additions & 3 deletions docs/usage.rst
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Overview
--------

Germline mutation rates are crucial parameters in genetics, genomics and
Germline mutation rates are important in genetics, genomics and
evolutionary biology. It is long known that mutation rates vary
substantially across the genome, but existing methods can only obtain
very rough estimates of local mutation rates and are difficult to be
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Citation
--------

Fang Y, Deng S, Li C. 2022. A generalizable deep learning framework for
inferring fine-scale germline mutation rate maps. *Nature Machine Intelligence* (2022)
Fang Y, Deng S, Li C. A generalizable deep learning framework for inferring
fine-scale germline mutation rate maps. *Nature Machine Intelligence* (2022)
`doi:10.1038/s42256-022-00574-5 <https://doi.org/10.1038/s42256-022-00574-5>`__

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