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 |
|---|---|---|
| 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 |
21 Nov 20, 2022
53 Nov 9, 2022
44 Oct 20, 2022
33 Dec 18, 2022
328 Dec 17, 2022
31 Oct 13, 2022
104 Nov 25, 2022
251 Dec 11, 2022
47 Jun 30, 2022
364 Dec 28, 2022
51 Nov 17, 2022
33 Dec 2, 2022
46 Dec 14, 2022
68 Nov 24, 2022
618 Dec 27, 2022
296 Dec 29, 2022
962 Dec 23, 2022
76 Dec 22, 2022
225 Dec 26, 2022