Bulk RNA sequencing time course pathway analysis progression visualization
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4 months ago
Fred • 0


I have bulk RNA sequencing data from a design as follows:

Control cells differentiating and sampled on day 0, 2, 4, and 6. Treatment group had a treatment from day 2 to 4 and sampled on day 4 and day 6 (all n = 3). (So 4 time points for control and 2 time points for treatment group).

I want to analyze the data by visualizing things with progression and not just day 2 versus day 0, day 4 versus day 0, etc. Is there a way to have a sort of pathway analysis progression or some alternative to show how things are progressing for the control and treatment conditions (something like the image below or similar)? I know this is done for single-cell data sets but I haven't found anything for bulk-RNA. I have tried using the 'gage' package but I'm not sure that is the correct way. Perhaps I should be sticking to simple comparisons? If you know of any literature or have any advice, I would greatly appreciate it! enter image description here

time-course RNA-seq pathway • 155 views

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