I have come across DESeq2
, edgeR
, and limma
for differential expression analysis in R
. I know that there are a large number of "helper" packages that enhance the functionality of these packages.
What are some other packages that are really popular and useful in this regard?
The ones I can think of are:
tximport
- data import.RUVSeq
- surrogate variable analysis.
EnhancedVolcano
for plotting.