Update CR2 reference

theislab · Oct 1, 2024 · 09a2333 · 09a2333
1 parent 9a710b8
commit 09a2333
Show file tree

Hide file tree

Showing 4 changed files with 45 additions and 30 deletions.
diff --git a/README.md b/README.md
@@ -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},
 }
 ```
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -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
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -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

diff --git a/docs/source/references.bib b/docs/source/references.bib
@@ -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},
 }
diff --git a/scvelo/inference/_metabolic_labeling.py b/scvelo/inference/_metabolic_labeling.py
@@ -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:
  ---------
@@ -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:
  ---------
@@ -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:
  ---------
@@ -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:
  ---------
@@ -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:
  ---------