Update docs (#1161)

* Update docstrings * Update `README.md` * Update `api.rst` Adds VELOVI and metabolic labeling inference. * Update `installation.rst` * Update `index.rst`
theislab · Dec 2, 2023 · 5132328 · 5132328
1 parent 632c60b
commit 5132328
Show file tree

Hide file tree

Showing 39 changed files with 291 additions and 177 deletions.
diff --git a/README.md b/README.md
@@ -13,16 +13,13 @@
 
 <img src="https://user-images.githubusercontent.com/31883718/67709134-a0989480-f9bd-11e9-8ae6-f6391f5d95a0.png" width="400px" align="left">
 
-**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
-[Bergen et al. (Nature Biotech, 2020](https://doi.org/10.1038/s41587-020-0591-3).
-
-RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
-scVelo generalizes the concept of RNA velocity
-[La Manno et al., Nature, 2018](https://doi.org/10.1038/s41586-018-0414-6>)
-by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
-transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
-
-scVelo is compatible with scanpy\_ and hosts efficient implementations of all RNA velocity models.
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells; RNA velocity
+enables the recovery of directed dynamic information by leveraging splicing kinetics
+<sup>[1](https://doi.org/10.1038/s41586-018-0414-6)</sup>. scVelo collects different
+methods for inferring RNA velocity using an expectation-maximization framework
+<sup>[2](https://doi.org/10.1038/s41587-020-0591-3)</sup>, deep generative modeling
+<sup>[3](https://doi.org/10.1038/s41592-023-01994-w)</sup>,
+or metabolically labeled transcripts<sup>[4](https://doi.org/10.1101/2023.07.19.549685)</sup>.
 
 ## scVelo's key applications
 
@@ -32,35 +29,72 @@ scVelo is compatible with scanpy\_ and hosts efficient implementations of all RN
 -   estimate reaction rates of transcription, splicing and degradation.
 -   use statistical tests, e.g., to detect different kinetics regimes.
 
-scVelo has, for instance, recently been used to study immune response in COVID-19
-patients and dynamic processes in human lung regeneration. Find out more in this list of
-[application examples](https://scholar.google.com/scholar?cites=18195185735875895912).
-
-## Latest news
-
--   Aug/2021: [Perspectives paper out in MSB](https://doi.org/10.15252/msb.202110282)
--   Feb/2021: scVelo goes multi-core
--   Dec/2020: Cover of [Nature Biotechnology](https://www.nature.com/nbt/volumes/38)
--   Nov/2020: Talk at [Single Cell Biology](https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/)
--   Oct/2020: [Helmholtz Best Paper Award](https://twitter.com/ICBmunich/status/1318611467722199041)
--   Oct/2020: Map cell fates with [CellRank](https://cellrank.org)
--   Sep/2020: Talk at [Single Cell Omics](https://twitter.com/fabian_theis/status/1305621028056465412)
--   Aug/2020: [scVelo out in Nature Biotech](https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html)
-
-## References
-
-[La Manno _et al._ (2018), RNA velocity of single cells, Nature](https://doi.org/10.1038/s41586-018-0414-6).
-
-[Bergen _et al._ (2020), Generalizing RNA velocity to transient cell states through dynamical modeling, Nature Biotech](https://doi.org/10.1038/s41587-020-0591-3).
-
-[Bergen _et al._ (2021), RNA velocity - current challenges and future perspectives, Molecular Systems Biology](https://doi.org/10.15252/msb.202110282).
+## Citing scVelo
+
+If you include or rely on scVelo when publishing research, please adhere to the
+following citation guide:
+
+### EM and steady-state model
+
+If you use the _EM_ (_dynamical_) or _steady-state model_, cite
+
+```bibtex
+@article{Bergen2020,
+  title = {Generalizing RNA velocity to transient cell states through dynamical modeling},
+  volume = {38},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-020-0591-3},
+  DOI = {10.1038/s41587-020-0591-3},
+  number = {12},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Bergen, Volker and Lange, Marius and Peidli, Stefan and Wolf, F. Alexander and Theis, Fabian J.},
+  year = {2020},
+  month = aug,
+  pages = {1408–1414}
+}
+```
+
+### veloVI
+
+If you use _veloVI_ (_VI model_), cite
+
+```bibtex
+@article{Gayoso2023,
+  title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
+  ISSN = {1548-7105},
+  url = {http://dx.doi.org/10.1038/s41592-023-01994-w},
+  DOI = {10.1038/s41592-023-01994-w},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron and Theis, Fabian J. and Yosef, Nir},
+  year = {2023},
+  month = sep
+}
+```
+
+### RNA velocity inference through metabolic labeling information
+
+If you use the implemented method for estimating RNA velocity from metabolic labeling
+information, cite
+
+```bibtex
+@article{Weiler2023,
+  title = {Unified fate mapping in multiview single-cell data},
+  url = {http://dx.doi.org/10.1101/2023.07.19.549685},
+  DOI = {10.1101/2023.07.19.549685},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe’er, Dana and Theis, Fabian J.},
+  year = {2023},
+  month = jul
+}
+```
 
 ## Support
 
 Found a bug or would like to see a feature implemented? Feel free to submit an
 [issue](https://github.com/theislab/scvelo/issues/new/choose).
 Have a question or would like to start a new discussion? Head over to
 [GitHub discussions](https://github.com/theislab/scvelo/discussions).
-In either case, you can also always send us an [email](mailto:mail@scvelo.org).
 Your help to improve scVelo is highly appreciated.
 For further information visit [scvelo.org](https://scvelo.org).
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -76,6 +76,7 @@ Tools (tl)
 
    tl.recover_dynamics
    tl.differential_kinetic_test
+   tl.VELOVI
 
 **Dynamical genes**
 
@@ -105,6 +106,18 @@ Tools (tl)
    tl.velocity_confidence
    tl.score_genes_cell_cycle
 
+Inference from metabolic labeling information
+---------
+
+.. autosummary::
+   :toctree: .
+
+   inference.get_labeling_time_mask
+   inference.get_labeling_times
+   inference.get_n_neighbors
+   inference.get_obs_dist_argsort
+   inference.get_parameters
+
 
 Plotting (pl)
 -------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -9,16 +9,12 @@ scVelo - RNA velocity generalized through dynamical modeling
 
 .. include:: _key_contributors.rst
 
-**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
-`Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
-
-RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
-scVelo generalizes the concept of RNA velocity
-(`La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
-by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
-transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
-
-scVelo is compatible with Scanpy_ and hosts efficient implementations of all RNA velocity models.
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells; RNA velocity
+enables the recovery of directed dynamic information by leveraging splicing kinetics
+:cite:p:`LaManno18`. scVelo collects different
+methods for inferring RNA velocity using an expectation-maximization framework
+:cite:p:`Bergen20`, deep generative modeling :cite:p:`Gayoso2023`,
+or metabolically labeled transcripts :cite:p:`Weiler2023`.
 
 scVelo's key applications
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -28,40 +24,77 @@ scVelo's key applications
 - estimate reaction rates of transcription, splicing and degradation.
 - use statistical tests, e.g., to detect different kinetics regimes.
 
-scVelo has, for instance, recently been used to study immune response in COVID-19
-patients and dynamic processes in human lung regeneration. Find out more in this list of
-`application examples <https://scholar.google.com/scholar?cites=18195185735875895912>`_.
 
-Latest news
-^^^^^^^^^^^
-- Aug/2021: `Perspectives paper out in MSB <https://doi.org/10.15252/msb.202110282>`_
-- Feb/2021: scVelo goes multi-core
-- Dec/2020: Cover of `Nature Biotechnology <https://www.nature.com/nbt/volumes/38>`_
-- Nov/2020: Talk at `Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>`_
-- Oct/2020: `Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>`_
-- Oct/2020: Map cell fates with `CellRank <https://cellrank.org>`_
-- Sep/2020: Talk at `Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>`_
-- Aug/2020: `scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>`_
+Citing scVelo
+^^^^^^^^^^^^^
+
+If you include or rely on scVelo when publishing research, please adhere to the
+following citation guide:
+
+**EM and steady-state model**
+
+If you use the *EM* (*dynamical*) or *steady-state model*, cite
+
+.. code-block:: bibtex
+
+    @article{Bergen2020,
+        title = {Generalizing RNA velocity to transient cell states through dynamical modeling},
+        volume = {38},
+        ISSN = {1546-1696},
+        url = {http://dx.doi.org/10.1038/s41587-020-0591-3},
+        DOI = {10.1038/s41587-020-0591-3},
+        number = {12},
+        journal = {Nature Biotechnology},
+        publisher = {Springer Science and Business Media LLC},
+        author = {Bergen, Volker and Lange, Marius and Peidli, Stefan and Wolf, F. Alexander and Theis, Fabian J.},
+        year = {2020},
+        month = aug,
+        pages = {1408–1414}
+    }
+
+
+**veloVI**
 
-References
-^^^^^^^^^^
-La Manno *et al.* (2018), RNA velocity of single cells, `Nature <https://doi.org/10.1038/s41586-018-0414-6>`_.
+If you use *veloVI* (*VI model*), cite
 
-Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
-`Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>`_.
+.. code-block:: bibtex
 
-Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives,
-`Molecular Systems Biology <https://doi.org/10.15252/msb.202110282>`_.
+    @article{Gayoso2023,
+        title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
+        ISSN = {1548-7105},
+        url = {http://dx.doi.org/10.1038/s41592-023-01994-w},
+        DOI = {10.1038/s41592-023-01994-w},
+        journal = {Nature Methods},
+        publisher = {Springer Science and Business Media LLC},
+        author = {Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron and Theis, Fabian J. and Yosef, Nir},
+        year = {2023},
+        month = sep
+    }
+
+**RNA velocity inference through metabolic labeling information**
+
+If you use the implemented method for estimating RNA velocity from metabolic labeling
+information, cite
+
+.. code-block:: bibtex
+
+    @article{Weiler2023,
+        title = {Unified fate mapping in multiview single-cell data},
+        url = {http://dx.doi.org/10.1101/2023.07.19.549685},
+        DOI = {10.1101/2023.07.19.549685},
+        publisher = {Cold Spring Harbor Laboratory},
+        author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe’er, Dana and Theis, Fabian J.},
+        year = {2023},
+        month = jul
+    }
 
 Support
 ^^^^^^^
 Found a bug or would like to see a feature implemented? Feel free to submit an
 `issue <https://github.com/theislab/scvelo/issues/new/choose>`_.
 Have a question or would like to start a new discussion? Head over to
 `GitHub discussions <https://github.com/theislab/scvelo/discussions>`_.
-In either case, you can also always send us an `email <mailto:mail@scvelo.org>`_.
 Your help to improve scVelo is highly appreciated.
-For further information visit `scvelo.org <https://scvelo.org>`_.
 
 
 .. toctree::
@@ -103,25 +136,12 @@ For further information visit `scvelo.org <https://scvelo.org>`_.
 .. |Docs| image:: https://readthedocs.org/projects/scvelo/badge/?version=latest
    :target: https://scvelo.readthedocs.io
 
-.. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=main
-   :target: https://travis-ci.org/theislab/scvelo
-
 .. _Scanpy: https://scanpy.readthedocs.io
 
-.. _calendly: https://calendly.com/scvelo
-
 .. |br| raw:: html
 
   <br/>
 
-.. |meet| raw:: html
-
-  <!-- Calendly link widget begin -->
-  <link href="https://assets.calendly.com/assets/external/widget.css" rel="stylesheet">
-  <script src="https://assets.calendly.com/assets/external/widget.js" type="text/javascript"></script>
-  <a href="" onclick="Calendly.initPopupWidget({url: 'https://calendly.com/scvelo'});return false;">here</a>
-  <!-- Calendly link widget end -->
-
 .. |dim| raw:: html
 
    <span class="__dimensions_badge_embed__" data-id="pub.1129830274" data-style="small_rectangle"></span>

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -19,12 +19,12 @@ Development Version
 
 To work with the latest development version, install from GitHub_ using::
 
-    pip install git+https://github.com/theislab/scvelo@develop
+    pip install git+https://github.com/theislab/scvelo@main
 
 or::
 
     git clone https://github.com/theislab/scvelo && cd scvelo
-    git checkout --track origin/develop
+    git checkout --track origin/main
     pip install -e .
 
 ``-e`` is short for ``--editable`` and links the package to the original cloned

diff --git a/docs/source/perspectives/index.rst b/docs/source/perspectives/index.rst
@@ -21,7 +21,6 @@ transcriptional boost in erythroid lineage, and misleading arrow projections in
 
 Notebook: `Perspectives <Perspectives>`_
 
-|
 Kinetic parameter analysis
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. image:: https://user-images.githubusercontent.com/31883718/130656606-00bd44be-9071-4008-be1b-244fa9c2d244.png

diff --git a/docs/source/references.bib b/docs/source/references.bib
@@ -62,3 +62,24 @@ @article{Wolf19
   title = {{PAGA}: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells},
   journal = {Genome Biology}
 }
+
+@article{Gayoso2023,
+  title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
+  url = {http://dx.doi.org/10.1038/s41592-023-01994-w},
+  doi = {10.1038/s41592-023-01994-w},
+  journal = {Nature Methods},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Adam Gayoso and Philipp Weiler and Mohammad Lotfollahi and Dominik Klein and Justin Hong and Aaron Streets and Fabian J. Theis and Nir Yosef},
+  year = {2023},
+  month = sep
+}
+
+@article{Weiler2023,
+  title = {Unified fate mapping in multiview single-cell data},
+  url = {http://dx.doi.org/10.1101/2023.07.19.549685},
+  DOI = {10.1101/2023.07.19.549685},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Philipp Weiler and Marius Lange and Michal Klein and Dana Pe{\textquotesingle}er and Fabian J. Theis},
+  year = {2023},
+  month = jul
+}