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|Stars| |PyPI| |PyPIDownloads| |Bioconda| |Docs| |
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MultiVelo - Velocity Inference from Single-Cell Multi-Omic Data |
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=============================================================== |
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Single-cell multi-omic datasets, in which multiple molecular modalities are profiled |
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within the same cell, provide a unique opportunity to discover the interplay between |
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cellular epigenomic and transcriptomic changes. To realize this potential, we developed |
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**MultiVelo**, a mechanistic model of gene expression that extends the popular RNA velocity |
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framework by incorporating epigenomic data. |
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MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate |
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parameters of gene regulation, providing a quantitative summary of the temporal relationship |
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between epigenomic and transcriptomic changes. Fitting MultiVelo on single-cell multi-omic |
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datasets revealed two distinct mechanisms of regulation by chromatin accessibility, quantified |
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the degree of concordance or discordance between transcriptomic and epigenomic states within |
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each cell, and inferred the lengths of time lags between transcriptomic and epigenomic changes. |
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Check out the :doc:`usage` section for further information. |
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.. toctree:: |
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:caption: Main |
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:maxdepth: 1 |
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:hidden: |
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usage |
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api |
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.. toctree:: |
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:caption: Demo |
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:maxdepth: 1 |
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:hidden: |
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MultiVelo_Demo |
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MultiVelo_Fig2 |
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MultiVelo_Fig3 |
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MultiVelo_Fig4 |
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MultiVelo_Fig5 |
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MultiVelo_Fig6 |
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adam_example |
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neural_net_example |
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.. |Stars| image:: https://img.shields.io/github/stars/welch-lab/multivelo?logo=GitHub&color=yellow |
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:target: https://github.com/welch-lab/multivelo/stargazers |
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.. |PyPI| image:: https://img.shields.io/pypi/v/multivelo?logo=PyPI |
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:target: https://pypi.org/project/multivelo |
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.. |PyPIDownloads| image:: https://pepy.tech/badge/multivelo |
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:target: https://pepy.tech/project/multivelo |
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.. |Bioconda| image:: https://img.shields.io/conda/dn/bioconda/multivelo?logo=Anaconda |
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:target: https://anaconda.org/bioconda/multivelo |
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.. |Docs| image:: https://readthedocs.org/projects/multivelo/badge/?version=latest |
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:target: https://multivelo.readthedocs.io |