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.
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.
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.
| Figure | nbviewer | Notebook Path |
|---|---|---|
| Fig. 1 | link | path |
| Fig. 2 | link | path |
| Fig. 3 | link | path |
| Fig. 4 | link | path |
| 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 |
| Extended Data Fig. 7 | link | path |
| Extended Data Fig. 8 | link | path |
| Extended Data Fig. 9 | link | path |
| 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 |
|---|---|---|
| Supplementary Tab. 1 | link | path |
| Supplementary Tab. 2 | link | path |
| Supplementary Tab. 3 | link | path |
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