Reproducibility

Here we feature a breakdown of analyses included in the manuscript associated with scdiffeq. While Figure 1 contains an overview that does not host any analyses, Figure 2 demonstrates the accuracy of scDiffEq compared to other contemporary models. Figure 3 demonstrates scDiffEq’s ability to impart in silico perturbations to cells then simulate and model the impact of that perturbation. Figure 4 describes our effort to study the interpretability of the model. In this figure, we highlight various aspects of model properties as they relate to the observed data.

Figure 2

Figure2A.ipynb

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Figure2B.ipynb

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Figure2D.ipynb

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Figure2E.ipynb

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Figure2F.ipynb

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Figure 3

Figure3AB.ipynb

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Figure3CD.ipynb

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Figure3EFG.v2.ipynb

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Figure3HI.ipynb

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Figure3J.ipynb

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Figure3J.make_supplementary_tables.ipynb

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Figure3KL.ipynb

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Figure3M.ipynb

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Figure 4

Figure4ABC.ipynb

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Figure4D.ipynb

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Figure4EF.ipynb

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Figure4G.ipynb

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Figure4HI.ipynb

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Figure4JKLM.ipynb

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Supplementary Figure 1

FigureS1.ipynb

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Supplementary Figure 2

FigureS2A.ipynb

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FigureS2B.ipynb

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FigureS2C.ipynb

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Supplementary Figure 3

FigureS3.ipynb

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Supplementary Figure 4

FigureS4.ipynb

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Supplementary Figure 5

FigureS5AB.ipynb

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FigureS5C.ipynb

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Supplementary Figure 7

FigureS7.ipynb

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Supplementary Figure 9

FigureS9.ipynb

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Supplementary Figure 10

FigureS10.ipynb

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Supplementary Figure 11

FigureS11.ipynb

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Supplementary Figure 12

FigureS12ABC.ipynb

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FigureS12D.ipynb

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FigureS12EFGHI.ipynb

_analyses/FigureS12EFGHI.ipynb