is possible to compare conditions?

[feanaros]

hi, I have a dataset of integrated KO + WT cells. Is it possible to split in some way the trajectories for each condition in R?

[RihaoQu]

Hi, this depends on your goal of analysis.
If you would like to compare the structure of the gene graph (or gene trajectories) between two different conditions, you will need to run GeneTrajectory on each condition (sample) separately.
If you would like to compare the gene dynamics between two conditions based on the common gene trajectory, like in Figure 5 in the manuscript, you only need to split the data object into two conditions after you generate the final gene bin scores. Then, you can visualize gene bin plots for each condition separately.