I have a time course dataset from RNAsequencing. Tipically it's bulk RNAseq, with 8 time-points and 3 replicates per sample. I was wondering if there is something like the "pseudo-time" from monocle package (single cell RNAseq) to order my sample on one dimension? In the PCA generated with Deseq2 plotPCA(rlog (DESeqDataSetFromMatrix), it seem to have a continuum between the sample in the axe 1. It's a differentiation process from primary cells. Problem is, as it's primary cells, activation between replicate is heterogeneous and I get for example Sample1-Day3 before Sample2-Day2.
So I would like to order sample without any a priori in one dimension. Do you know if there is a soft that can do that? Thanks a lot, Nicolas