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Backport PR #1463 on branch 0.15.x (Peakvi ref update) #1465

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Mar 28, 2022
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Backport PR #1463 on branch 0.15.x (Peakvi ref update) #1465

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8 changes: 4 additions & 4 deletions docs/references.rst
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@@ -1,6 +1,10 @@
References
----------

.. [Ashuach22] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2022),
*PeakVI: A deep generative model for single-cell chromatin accessibility analysis*,
`Cell Reports Methods <https://doi.org/10.1016/j.crmeth.2022.100182>`__.

.. [Gayoso22] Adam Gayoso*, Romain Lopez*, Galen Xing*, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-Lopez, Lior Pachter, Fabian J Theis, Aaron Streets, Michael I Jordan, Jeffrey Regier, and Nir Yosef (2022),
*A Python library for probabilistic analysis of single-cell omics data*,
`Nature Biotechnology <http://dx.doi.org/10.1038/s41587-021-01206-w>`__.
Expand All @@ -13,10 +17,6 @@ References
*Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation*,
`biorxiv <https://www.biorxiv.org/content/10.1101/2021.04.28.441833v1>`__.

.. [Ashuach21] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2021),
*PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis*,
`biorxiv <https://www.biorxiv.org/content/10.1101/2021.04.29.442020v1>`__.

.. [AshuachGabitto21] Tal Ashauch*, Mariano I Gabitto*, Michael I Jordan, Nir Yosef (2021),
*MultiVI: deep generative model for the integration of multi-modal data*,
`biorxiv <https://www.biorxiv.org/content/10.1101/2021.08.20.457057v1>`__.
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2 changes: 1 addition & 1 deletion docs/user_guide/index.md
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Expand Up @@ -50,7 +50,7 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In
- Reference
- Tasks
* - :doc:`/user_guide/models/peakvi`
- [Ashuach21]_
- [Ashuach22]_
- Dimensionality reduction, removal of unwanted variation, integration across replicates, donors, and technologies, differential expression, imputation, normalization of other cell- and sample-level confounding factors
```

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2 changes: 1 addition & 1 deletion scvi/model/_peakvi.py
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Expand Up @@ -35,7 +35,7 @@

class PEAKVI(ArchesMixin, VAEMixin, UnsupervisedTrainingMixin, BaseModelClass):
"""
Peak Variational Inference [Ashuach21]_
Peak Variational Inference [Ashuach22]_
Parameters
----------
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