So I have my time series RNA-seq data, which I conducted some k-means clustering on in R to have a look at how it clusters. I am wondering if there are any good tools in R to then analyse the genes within each cluster, or the next step from the k-means clustering? Each cluster has around 50 genes in them.
I've been thinking about investigating nearby transcription factors (mouse cells) however the closest R tool I can find for doing that is pwOmics. I know that the TFcheckpoint webtool is a thing, however I was hoping to avoid copy-pasting forty different sets of genes in there from text files. Are there any similar R tools?
The main thing is that I am a bit unsure where to go from here, as there are a lot of genes within each cluster, and I have about four different plots with about 10 clusters in each. Any suggestions would be super useful! Thanks