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

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Marius1311 merged 9 commits intomainfrom
readme/related-packages
Mar 9, 2026
Merged

Add related packages to README, update bib entries, remove cellrank.org references#1312
Marius1311 merged 9 commits intomainfrom
readme/related-packages

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Summary

Housekeeping PR with three changes:

1. Add "Related packages" section to README

Compact table listing 6 sibling packages (moscot, moslin, VeloVI, RegVelo, CellMapper, CellAnnotator) with links to docs and references. Notes scverse ecosystem membership.

2. Update references.bib

  • moscot (klein:23klein:25): updated from bioRxiv preprint to published Nature 638, 1065–1075 (2025), with full 20-author list.
  • moslin (lange:23lange:24): updated from bioRxiv preprint to published Genome Biology 25 (2024).
  • Added VeloVI (gayoso:24): Nature Methods 21, 50–59 (2024).
  • Added RegVelo (wang:24): bioRxiv (2024).
  • Updated :cite: reference in RealTimeKernel.from_moscot() docstring.

3. Remove outdated cellrank.org references

  • Replaced cellrank.org URLs with cellrank.readthedocs.io/en/latest/.
  • Removed v1→v2 migration banner from Sphinx config and docs index.
  • Renamed "Moving to CellRank 2" page to "Moving from v1 to v2".

@Marius1311 Marius1311 force-pushed the readme/related-packages branch 3 times, most recently from 3b31436 to 52d6b5c Compare March 9, 2026 13:58
@Marius1311 Marius1311 force-pushed the readme/related-packages branch from 52d6b5c to b9666c5 Compare March 9, 2026 13:59
@Marius1311 Marius1311 merged commit 88b438a into main Mar 9, 2026
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@Marius1311 Marius1311 deleted the readme/related-packages branch March 9, 2026 14:26
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