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. 1 | link | path |
| Fig. 2 | link | 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 |
|---|---|---|
| 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 |
| Extended Data Fig. 5 | link | path |
| Extended Data Fig. 6 | link | path |
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| Extended Data Fig. 10 | link | path |
| Figure | nbviewer | Notebook Path |
|---|---|---|
| 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 |
| Supplementary Fig. 6 | link | path |
| Supplementary Fig. 7 | link | path |
| Supplementary Fig. 8 | link | path |
| Supplementary Fig. 9 | link | path |
| Supplementary Fig. 10 | link | path |
| 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 |
125 Dec 22, 2022
46 Sep 05, 2022
0 Mar 20, 2022
3 Sep 19, 2022
17 Dec 01, 2022
820 Dec 17, 2022
2 Feb 14, 2022
63 Dec 18, 2022
2.1k Jan 04, 2023
58 Dec 12, 2022
112 Dec 28, 2022
182 Dec 29, 2022
2 Jan 25, 2022
869 Jan 06, 2023
10 Sep 30, 2022
35 Nov 25, 2022
1 Dec 02, 2021
19 Sep 08, 2022
2 Mar 27, 2022
17 Jul 07, 2022