I have been using Monocole2 to study the progression of cells into a disease state and have had good results clustering the cells, identifying deferentially expressed genes, and plotting a pseudotime continuum.
However, I would also like to identify genes that are critical to the initial transition from healthy to disease state. I figure these should logically be the genes that have significantly increased or decreased expression at the earliest point in psuedotime where the diseased cells start showing up. However I do not know how to systemically identify these genes.
Monocole2 offers a great way to plot a heatmap of gene expression in pesudotime (the plot_pseudotime_heatmap function). However, it is hard to do proper quantitative analysis using this heatmap. Is there anyway to get the matrix directly used to make this heatmap or any other data set showing the expression of all genes in pseudotime?
Thanks a lot for your time and attention!
