Add related packages to README, update bib entries, remove cellrank.org references (#1312)

Marius1311 · web-flow · commit 88b438af9997 · 2026-03-09T15:26:53.000+01:00
* Add related packages section to README and update bib entries

* Replace cellrank.org URLs with cellrank.readthedocs.io

* Remove v1-to-v2 migration banner and rename version2 page

* Unify docs landing page with README via {include}

* Update package maintainers

* Enable sphinx autobuild

* Update teams page

* Update teams page
diff --git a/README.md b/README.md
@@ -8,16 +8,18 @@
 
 # CellRank 2: Unified fate mapping in multiview single-cell data
 
+<!-- image-start -->
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset="docs/_static/img/dark_mode_overview.png">
-  <img alt="CellRank overview" src="docs/_static/img/light_mode_overview.png" width="600px" align="center">
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/scverse/cellrank/main/docs/_static/img/dark_mode_overview.png">
+  <img alt="CellRank overview" src="https://raw.githubusercontent.com/scverse/cellrank/main/docs/_static/img/light_mode_overview.png" width="600px" align="center">
 </picture>
+<!-- image-end -->
 
 **CellRank** is a modular framework to study cellular dynamics based on Markov state modeling of
 multi-view single-cell data. See our [documentation], and the [CellRank 1] and [CellRank 2] manuscripts to learn more.
+Read a summary of the CellRank papers [here](https://cellrank.readthedocs.io/en/latest/about/cite.html#cellrank-papers).
 
-> [!IMPORTANT]
-> Please refer to [our citation guide](https://cellrank.readthedocs.io/en/latest/about/cite.html) to cite our software correctly.
+⚠️ **Please refer to [our citation guide](https://cellrank.readthedocs.io/en/latest/about/cite.html) to cite our software correctly.**
 
 CellRank scales to large cell numbers, is fully compatible with the [scverse] ecosystem, and is easy to use.
 In the backend, it is powered by [pyGPCCA] ([Reuter et al. (2018)]). Feel
@@ -41,12 +43,38 @@ pip install cellrank
 
 See the [installation guide](https://cellrank.readthedocs.io/en/latest/installation.html) for more options.
 
+## Related packages
+
+If you like CellRank, check out these packages from the same authors.
+Almost all are part of the [scverse ecosystem].
+
+| Package | Description | Reference |
+|---------|-------------|-----------|
+| [moscot] | Optimal transport for temporal, spatial, and spatio-temporal single-cell mapping | [Klein et al. (2025)] |
+| [moslin] | Trajectory inference with lineage barcodes via optimal transport (part of moscot) | [Lange et al. (2024)] |
+| [VeloVI] | RNA velocity with variational inference and uncertainty quantification (part of scvi-tools) | [Gayoso et al. (2024)] |
+| [RegVelo] | Jointly learning gene regulation and RNA velocity | [Wang et al. (2024)] |
+| [CellMapper] | kNN-based label, embedding, and molecular layer transfer between datasets | — |
+| [CellAnnotator] | LLM-based cell type annotation with support for major LLM providers | — |
+
+[moscot]: https://moscot.readthedocs.io/
+[moslin]: https://moscot.readthedocs.io/en/latest/notebooks/tutorials/100_lineage.html
+[VeloVI]: https://docs.scvi-tools.org/en/1.3.3/tutorials/notebooks/scrna/velovi.html
+[RegVelo]: https://regvelo.readthedocs.io/
+[CellMapper]: https://cellmapper.readthedocs.io/
+[CellAnnotator]: https://cell-annotator.readthedocs.io/
+[scverse ecosystem]: https://scverse.org/packages/#ecosystem
+[Klein et al. (2025)]: https://doi.org/10.1038/s41586-024-08453-2
+[Lange et al. (2024)]: https://doi.org/10.1186/s13059-024-03422-4
+[Gayoso et al. (2024)]: https://doi.org/10.1038/s41592-023-01994-w
+[Wang et al. (2024)]: https://doi.org/10.1101/2024.12.11.627935
+
 [La Manno et al. (2018)]: https://doi.org/10.1038/s41586-018-0414-6
 [Bergen et al. (2020)]: https://doi.org/10.1038/s41587-020-0591-3
 [Reuter et al. (2018)]: https://doi.org/10.1021/acs.jctc.8b00079
 [scverse]: https://scverse.org/
 [pyGPCCA]: https://github.com/msmdev/pyGPCCA
 [CellRank 1]: https://www.nature.com/articles/s41592-021-01346-6
 [CellRank 2]: https://doi.org/10.1038/s41592-024-02303-9
-[documentation]: https://cellrank.org
+[documentation]: https://cellrank.readthedocs.io/en/latest/
 [issue]: https://github.com/theislab/cellrank/issues/new/choose
diff --git a/docs/about/team.md b/docs/about/team.md
@@ -2,7 +2,7 @@
 
 CellRank was started as a collaboration between the Theis lab at Helmholtz Munich and the Pe'er lab at Memorial Sloan
 Kettering Cancer Center (MSKCC). We are happy about every code contribution we received so far, check out the
-[contributions](https://github.com/theislab/cellrank/graphs/contributors) section on GitHub for an overview.
+[contributions](https://github.com/theislab/cellrank/graphs/contributors) section on GitHub for an overview. CellRank is now part of the [scVerse GitHub organization](https://github.com/scverse).
 
 ## Principal Investigators
 
@@ -29,6 +29,13 @@ Kettering Cancer Center (MSKCC). We are happy about every code contribution we r
 ```{eval-rst}
 .. grid:: auto
 
+    .. grid-item-card:: :fab:`twitter` `Marius Lange <https://twitter.com/MariusLange8>`_
+        :img-top: https://avatars.githubusercontent.com/Marius1311
+
+        - :fas:`house` `mariuslange.com <https://mariuslange.com/>`_
+        - :fas:`graduation-cap` `Google Scholar <https://scholar.google.com/citations?user=QrhWUR4AAAAJ>`__
+        - :fab:`github` `Marius1311 <https://github.com/Marius1311>`_
+
     .. grid-item-card:: :fab:`twitter` `Philipp Weiler <https://twitter.com/philippweiler7>`_
         :img-top: https://avatars.githubusercontent.com/u/28675704
 
@@ -40,13 +47,6 @@ Kettering Cancer Center (MSKCC). We are happy about every code contribution we r
 
         - :fas:`graduation-cap` `Google Scholar <https://scholar.google.com/citations?user=zByzdzcAAAAJ>`__
         - :fab:`github` `michalk8 <https://github.com/michalk8>`_
-
-    .. grid-item-card:: :fab:`twitter` `Marius Lange <https://twitter.com/MariusLange8>`_
-        :img-top: https://mariuslange.com/author/marius-lange/avatar_huc2ea0f123de6d091882f094508aad23f_1614639_270x270_fill_q75_lanczos_center.jpg
-
-        - :fas:`house` `mariuslange.com <https://mariuslange.com/>`_
-        - :fas:`graduation-cap` `Google Scholar <https://scholar.google.com/citations?user=QrhWUR4AAAAJ>`__
-        - :fab:`github` `Marius1311 <https://github.com/Marius1311>`_
 ```
 
 ## `pyGPCCA` Development
diff --git a/docs/about/version2.md b/docs/about/version2.md
@@ -1,4 +1,4 @@
-# Moving to CellRank 2
+# Moving from v1 to v2
 
 The original CellRank version (v1) {cite}`lange:22` was a framework to analyze cellular dynamics based on RNA velocity
 {cite}`manno:18,bergen:20` and gene expression similarity. Based on a
@@ -38,7 +38,7 @@ We outline the most important changes here. For a more detailed account, please
 - Removal of the `cellrank.external`: anyone wishing to contribute to CellRank can do this now directly via
   {mod}`cellrank.kernels` and {mod}`cellrank.estimators`. We welcome any contribution to CellRank,
   see our {doc}`contribution guide <../contributing>`, and feel free to get in touch via an
-  [issue](https://github.com/theislab/cellrank/issues/new/choose) or [email](mailto:info@cellrank.org).
+  [issue](https://github.com/theislab/cellrank/issues/new/choose).
 - Replacement of the old `cellrank.external.WOTKernel` with a new {class}`cellrank.kernels.RealTimeKernel`: this is
   CellRank's interface with {mod}`moscot`, enabling us to analyze large-scale time-course studies with additional
   spatial or lineage readout {cite}`klein:23,lange:23`. In addition, the {class}`~cellrank.kernels.RealTimeKernel`
diff --git a/docs/conf.py b/docs/conf.py
@@ -157,8 +157,6 @@
 html_show_sphinx = False
 html_show_sourcelink = False
 html_theme_options = {
-    "announcement": "If you're moving from CellRank v1 to v2, "
-    "see our <a href='https://cellrank.readthedocs.io/en/latest/about/version2.html'>notes on important changes</a>.",
     "sidebar_hide_name": True,
     "light_logo": "img/light_mode_logo.png",
     "dark_logo": "img/dark_mode_logo.png",
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -261,15 +261,28 @@ hatch run docs:build
 hatch run docs:open
 ```
 
+For live preview with auto-rebuild on save:
+
+```bash
+hatch run docs:auto
+```
+
 ::::
 
 ::::{tab-item} uv
 :sync: uv
 
 ```bash
-cd docs
-uv run sphinx-build -M html . _build
-open _build/html/index.html  # macOS; use xdg-open on Linux
+uv sync --group docs
+source .venv/bin/activate
+sphinx-build -M html docs docs/_build
+open docs/_build/html/index.html  # macOS; use xdg-open on Linux
+```
+
+For live preview with auto-rebuild on save:
+
+```bash
+sphinx-autobuild docs docs/_build/html --open-browser --watch README.md
 ```
 
 ::::
diff --git a/docs/index.md b/docs/index.md
@@ -1,40 +1,6 @@
----
-substitutions:
-  CI: |-
-    ```{image} https://img.shields.io/github/actions/workflow/status/theislab/cellrank/test.yml?branch=main
-    :alt: CI
-    :target: https://github.com/theislab/cellrank/actions
-    ```
-  Codecov: |-
-    ```{image} https://codecov.io/gh/theislab/cellrank/branch/main/graph/badge.svg
-    :alt: Coverage
-    :target: https://codecov.io/gh/theislab/cellrank
-    ```
-  Discourse: |-
-    ```{image} https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org
-    :alt: Discourse
-    :target: https://discourse.scverse.org/c/ecosystem/cellrank/
-    ```
-  Docs: |-
-    ```{image} https://img.shields.io/readthedocs/cellrank
-    :alt: Documentation
-    :target: https://cellrank.readthedocs.io/
-    ```
-  Downloads: |-
-    ```{image} https://static.pepy.tech/badge/cellrank
-    :alt: Downloads
-    :target: https://pepy.tech/project/cellrank
-    ```
-  PyPI: |-
-    ```{image} https://img.shields.io/pypi/v/cellrank.svg
-    :alt: PyPI
-    :target: https://pypi.org/project/cellrank
-    ```
----
-
-{{ PyPI }} {{ Downloads }} {{ CI }} {{ Docs }} {{ Codecov }} {{ Discourse }}
-
-# CellRank 2: Unified fate mapping in multiview single-cell data
+```{include} ../README.md
+:end-before: <!-- image-start -->
+```
 
 ```{image} _static/img/light_mode_overview.png
 :align: center
@@ -48,46 +14,9 @@ substitutions:
 :width: 600px
 ```
 
-**CellRank** {cite}`lange:22,weiler:24` is a modular framework to study cellular dynamics based on Markov state modeling of
-multi-view single-cell data. See {doc}`about CellRank <about/index>` to learn more and {doc}`our citation guide <about/cite>` for guidance on
-citing our work correctly. Two peer-reviewed publications accompany our software:
-
-- [CellRank for directed single-cell fate mapping](https://doi.org/10.1038/s41592-021-01346-6)
-- [CellRank 2: unified fate mapping in multiview single-cell data](https://doi.org/10.1038/s41592-024-02303-9)
-
-:::{important}
-Please refer to {doc}`our citation guide <about/cite>` to cite our software correctly.
-:::
-
-CellRank scales to large cell numbers, is fully compatible with the [scverse] ecosystem, and is easy to use. In the
-backend, it is powered by the [pyGPCCA package](https://github.com/msmdev/pyGPCCA) {cite}`reuter:19,reuter:22`. Feel
-free to open an [issue] if you encounter a bug, need our help or just want to make a comment/suggestion.
-
-:::{important}
-If you're moving from CellRank 1 to CellRank 2, check out {doc}`../about/version2`.
-:::
-
-## CellRank's key applications
-
-- Estimate differentiation direction based on a varied number of biological priors, including
-  {doc}`pseudotime <notebooks/tutorials/kernels/300_pseudotime>`,
-  {doc}`developmental potential <notebooks/tutorials/kernels/400_cytotrace>`,
-  {doc}`RNA velocity <notebooks/tutorials/kernels/200_rna_velocity>`,
-  {doc}`experimental time points <notebooks/tutorials/kernels/500_real_time>`, and {mod}`more <cellrank.kernels>`.
-- Compute initial, terminal and intermediate {doc}`macrostates <notebooks/tutorials/estimators/600_initial_terminal>`
-  {cite}`reuter:19,reuter:22`.
-- Infer {doc}`fate probabilities and driver genes <notebooks/tutorials/estimators/700_fate_probabilities>`.
-- Visualize and cluster {doc}`gene expression trends <notebooks/tutorials/estimators/800_gene_trends>`.
-- ... and much more, check out our {doc}`API <api/index>`.
-
-## Getting started with CellRank
-
-We have {doc}`notebooks/tutorials/index` to help you getting started. To see CellRank in action, explore our
-manuscripts {cite}`lange:22,weiler:24` in Nature Methods.
-
-## Contributing
-
-We actively encourage any contribution! To get started, please check out the {doc}`contributing`.
+```{include} ../README.md
+:start-after: <!-- image-end -->
+```
 
 ```{toctree}
 :caption: General
@@ -114,6 +43,3 @@ about/team
 GitHub <https://github.com/theislab/cellrank>
 Discourse <https://discourse.scverse.org/c/ecosytem/cellrank/40>
 ```
-
-[issue]: https://github.com/theislab/cellrank/issues/new/choose
-[scverse]: https://scverse.org/
diff --git a/docs/references.bib b/docs/references.bib
@@ -526,14 +526,14 @@ @article{zhang:14
   year      = {2014},
 }
 
-@article{klein:23,
-  author    = {Klein, Dominik and Palla, Giovanni and Lange, Marius and Klein, Michal and Piran, Zoe and Gander, Manuel and Meng-Papaxanthos, Laetitia and Sterr, Michael and Bastidas-Ponce, Aimée and Tarquis-Medina, Marta and Lickert, Heiko and Bakhti, Mostafa and Nitzan, Mor and Cuturi, Marco and Theis, Fabian J.},
-  publisher = {Cold Spring Harbor Laboratory},
-  url       = {https://www.biorxiv.org/content/early/2023/05/12/2023.05.11.540374},
-  doi       = {10.1101/2023.05.11.540374},
-  journal   = {bioRxiv},
+@article{klein:25,
+  author    = {Klein, Dominik and Palla, Giovanni and Lange, Marius and Klein, Michal and Piran, Zoe and Gander, Manuel and Meng-Papaxanthos, Laetitia and Sterr, Michael and Saber, Lama and Jing, Changying and Bastidas-Ponce, Aim\'{e}e and Cota, Perla and Tarquis-Medina, Marta and Parikh, Shrey and Gold, Ilan and Lickert, Heiko and Bakhti, Mostafa and Nitzan, Mor and Cuturi, Marco and Theis, Fabian J.},
+  doi       = {10.1038/s41586-024-08453-2},
+  journal   = {Nature},
+  pages     = {1065--1075},
   title     = {Mapping cells through time and space with moscot},
-  year      = {2023},
+  volume    = {638},
+  year      = {2025},
 }
 
 @article{cuturi:13,
@@ -545,14 +545,13 @@ @article{cuturi:13
   year    = {2013},
 }
 
-@article{lange:23,
-  author    = {Lange, Marius and Piran, Zoe and Klein, Michal and Spanjaard, Bastiaan and Klein, Dominik and Junker, Jan Philipp and Theis, Fabian J and Nitzan, Mor},
-  publisher = {Cold Spring Harbor Laboratory},
-  doi       = {10.1101/2023.04.14.536867},
-  journal   = {bioRxiv},
-  pages     = {2023--04},
+@article{lange:24,
+  author    = {Lange, Marius and Piran, Zoe and Klein, Michal and Spanjaard, Bastiaan and Klein, Dominik and Junker, Jan Philipp and Theis, Fabian J. and Nitzan, Mor},
+  doi       = {10.1186/s13059-024-03422-4},
+  journal   = {Genome Biology},
   title     = {Mapping lineage-traced cells across time points with moslin},
-  year      = {2023},
+  volume    = {25},
+  year      = {2024},
 }
 
 @article{chizat:18,
@@ -825,3 +824,21 @@ @article{weiler:25
   title     = {CellRank: consistent and data view agnostic fate mapping for single-cell genomics},
   year      = {2026},
 }
+
+@article{gayoso:24,
+  author    = {Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron M. and Theis, Fabian J. and Yosef, Nir},
+  doi       = {10.1038/s41592-023-01994-w},
+  journal   = {Nature Methods},
+  pages     = {50--59},
+  title     = {Deep generative modeling of transcriptional dynamics for {RNA} velocity analysis in single cells},
+  volume    = {21},
+  year      = {2024},
+}
+
+@article{wang:24,
+  author    = {Wang, Weixu and Hu, Zhiyuan and Weiler, Philipp and Mayes, Sarah and Lange, Marius and Wang, Jingye and Xue, Zhengyuan and Sauka-Spengler, Tatjana and Theis, Fabian J.},
+  doi       = {10.1101/2024.12.11.627935},
+  journal   = {bioRxiv},
+  title     = {{RegVelo}: gene-regulatory-informed dynamics of single cells},
+  year      = {2024},
+}
diff --git a/pyproject.toml b/pyproject.toml
@@ -16,7 +16,8 @@ keywords = [
 license = "BSD-3-Clause"
 license-files = [ "LICENSE" ]
 maintainers = [
-  { name = "Michal Klein", email = "info@cellrank.org" },
+  { name = "Marius Lange", email = "mlange@ethz.ch" },
+  { name = "Philipp Weiler" },
 ]
 
 authors = [
@@ -93,6 +94,7 @@ docs = [
   "furo>=2024.8.6",
   "myst-nb>=1.2",
   "sphinx>=7.4",
+  "sphinx-autobuild",
   "sphinx-autodoc-typehints>=2.5",
   "sphinx-copybutton>=0.5",
   "sphinx-design>=0.6",
@@ -132,6 +134,7 @@ dependency-groups = [ "docs" ]
 scripts.build = "sphinx-build -M html docs docs/_build {args}"
 scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
+scripts.auto = "sphinx-autobuild docs docs/_build/html --open-browser --watch README.md {args}"
 
 [tool.ruff]
 line-length = 120
diff --git a/src/cellrank/kernels/_real_time_kernel.py b/src/cellrank/kernels/_real_time_kernel.py
@@ -218,7 +218,7 @@ def from_moscot(
         copy: bool = False,
         **kwargs: Any,
     ) -> "RealTimeKernel":
-        """Construct the kernel from :mod:`moscot` :cite:`klein:23`.
+        """Construct the kernel from :mod:`moscot` :cite:`klein:25`.
 
         Parameters
         ----------
