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Update CR2 reference #1277

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Update CR2 reference #1277

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21 changes: 13 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -61,14 +61,19 @@ If you use the implemented method for estimating RNA velocity from metabolic lab
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
@article{Weiler2024,
author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe'er, Dana and Theis, Fabian},
publisher = {Springer Science and Business Media LLC},
url = {http://dx.doi.org/10.1038/s41592-024-02303-9},
doi = {10.1038/s41592-024-02303-9},
issn = {1548-7105},
journal = {Nature Methods},
month = jun,
number = {7},
pages = {1196--1205},
title = {CellRank 2: unified fate mapping in multiview single-cell data},
volume = {21},
year = {2024},
}
```

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23 changes: 14 additions & 9 deletions docs/source/index.rst
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Expand Up @@ -14,7 +14,7 @@ enables the recovery of directed dynamic information by leveraging splicing kine
: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`.
or metabolically labeled transcripts :cite:p:`Weiler2024`.

scVelo's key applications
^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -59,14 +59,19 @@ 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
@article{Weiler2024,
author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe'er, Dana and Theis, Fabian},
publisher = {Springer Science and Business Media LLC},
url = {http://dx.doi.org/10.1038/s41592-024-02303-9},
doi = {10.1038/s41592-024-02303-9},
issn = {1548-7105},
journal = {Nature Methods},
month = jun,
number = {7},
pages = {1196--1205},
title = {CellRank 2: unified fate mapping in multiview single-cell data},
volume = {21},
year = {2024},
}

Support
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21 changes: 13 additions & 8 deletions docs/source/references.bib
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Expand Up @@ -74,12 +74,17 @@ @article{Gayoso2023
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
@article{Weiler2024,
author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe'er, Dana and Theis, Fabian},
publisher = {Springer Science and Business Media LLC},
url = {http://dx.doi.org/10.1038/s41592-024-02303-9},
doi = {10.1038/s41592-024-02303-9},
issn = {1548-7105},
journal = {Nature Methods},
month = jun,
number = {7},
pages = {1196--1205},
title = {CellRank 2: unified fate mapping in multiview single-cell data},
volume = {21},
year = {2024},
}
10 changes: 5 additions & 5 deletions scvelo/inference/_metabolic_labeling.py
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Expand Up @@ -143,7 +143,7 @@ def _get_n_neighbors(
def get_labeling_times(adata, time_key) -> List:
"""Get labeling times in dataset.

See :cite:p:`Weiler2023`.
See :cite:p:`Weiler2024`.

Arguments:
---------
Expand All @@ -164,7 +164,7 @@ def get_labeling_time_mask(
) -> Dict[float, np.ndarray]:
"""Get number of neighbors required to include ``n_nontrivial_counts`` counts per labeling time.

See :cite:p:`Weiler2023`.
See :cite:p:`Weiler2024`.

Arguments:
---------
Expand All @@ -191,7 +191,7 @@ def get_obs_dist_argsort(
) -> Dict[float, np.ndarray]:
"""Calculate argsorted pairwise distances per labeling_time_point.

See :cite:p:`Weiler2023`.
See :cite:p:`Weiler2024`.

Arguments:
---------
Expand Down Expand Up @@ -232,7 +232,7 @@ def get_n_neighbors(
) -> Dict[str, pd.DataFrame]:
"""Get number of neighbors required to include ``n_nontrivial_counts`` counts per labeling time.

See :cite:p:`Weiler2023`.
See :cite:p:`Weiler2024`.

Arguments:
---------
Expand Down Expand Up @@ -389,7 +389,7 @@ def get_parameters(
):
"""Estimates parameters of splicing kinetics from metabolic labeling data.

See :cite:p:`Weiler2023`.
See :cite:p:`Weiler2024`.

Arguments:
---------
Expand Down
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