CellRank's reproducibility repository
We believe that reproducibility is key and have made it as simple as possible to reproduce our results. Please either open an issue or contact as at [email protected] should you experience difficulties reproducing any result.
Manuscript, code and data
CellRank is published in Nature Methods and the software package can be found at our main website, cellrank.org. Raw published data is available from the Gene Expression Omnibus (GEO) under accession codes:
Processed data, including spliced and unspliced count abundances, is available on figshare. To ease reproducibility, our data examples can also be accessed through CellRank's dataset interface.
Navigating this repository
We've organized this repository along the categories below. For each item, you can click the link under nbviewer to open the notebook in the browser using nbviewer. There is no 1-1 mapping from figures to notebooks - some notebooks produce panels for several figures, and some figures contain panels from several notebooks. The tables we provide here make the connection between figures and notebooks explicit. At the top of each notebook, we indicate the package versions we use.
Results
Main Figures| Figure | nbviewer | Notebook Path |
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| Fig. 5 Palantir | link | path |
| Fig. 5 STEMNET | link | path |
| Fig. 5 Velocyto | link | path |
| Fig. 5 FateID | link | path |
| Fig. 6 | link | path |
| Figure | nbviewer | Notebook Path |
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| Extended Data Fig. 1 | NA (toy data) | NA (toy data) |
| Extended Data Fig. 2 | link | path |
| Extended Data Fig. 3 | link | path |
| Extended Data Fig. 4 | link | path |
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| Extended Data Fig. 10 | link | path |
| Figure | nbviewer | Notebook Path |
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| Supplementary Fig. 1 | link | path |
| Supplementary Fig. 2 | link | path |
| Supplementary Fig. 3 | link | path |
| Supplementary Fig. 4 | link | path |
| Supplementary Fig. 5 | link | path |
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| Supplementary Fig. 11 | link | path |
| Supplementary Fig. 12 | link1 link2 | path1 path2 |
| Supplementary Fig. 13 | link | path |
| Supplementary Fig. 14 | link | path |
| Supplementary Fig. 15 | link | path |
| Supplementary Fig. 16 | link | path |
| Supplementary Fig. 17 | NA (microscopy results) | NA (microscopy results) |
| Table | nbviewer | Notebook Path |
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| Supplementary Tab. 1 | link | path |
| Supplementary Tab. 2 | link | path |
| Supplementary Tab. 3 | link | path |
1 Dec 13, 2021
281 Dec 31, 2022
34 Dec 14, 2022
44 Jul 10, 2022
26 Dec 21, 2022
178 Dec 02, 2022
50 Dec 29, 2022
7 Dec 12, 2022
10 Jun 17, 2022
1.4k Dec 25, 2022
86 Dec 07, 2022
3 Apr 20, 2022
97 Dec 28, 2022
2 Sep 29, 2022
5 Jul 26, 2022
731 Jan 01, 2023
1.4k Dec 29, 2022
146 Nov 29, 2022
22 Dec 21, 2022
93 Dec 25, 2022