From 09a2333de598dd20cee389fcf4b03a72307d1cd0 Mon Sep 17 00:00:00 2001 From: Philipp Weiler Date: Tue, 1 Oct 2024 08:01:54 +0200 Subject: [PATCH] Update CR2 reference --- README.md | 21 +++++++++++++-------- docs/source/index.rst | 23 ++++++++++++++--------- docs/source/references.bib | 21 +++++++++++++-------- scvelo/inference/_metabolic_labeling.py | 10 +++++----- 4 files changed, 45 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 5f4ec650..14a59570 100644 --- 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 index 772e7e32..41a4331b 100644 --- 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 index 14bab723..bbfd5783 100644 --- 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 index 9987404c..1e7d40cc 100644 --- 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: ---------