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I have single cell data from two samples : normal and pathological and I would like to track the progression of the cells (and find the genes that drive it) from normal to pathological.

Upon first glance, it seems most reasonable to define the trajectory in advance in such a way that it would have a starting point, an end point, and a straight route between these two. Is it possible, and using what package if so?

P.S. In contrast to the question above - I started with the destiny Bioconductor package. However, it always yields three tips for the diffusion pseudotime, and I am not sure how to determine the starting and the end tip of the trajectory...

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slingshot (Bioconductor) accepts a priori starts and ends. For differential expression along the trajectory you may check tradeSeq.

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