Hi,

Is DESeq2 capable of estimating the differential expression between samples of the same group (for example, JUST in the Control group without the treatment group)?

Could you please describe how?

DESeq2 will assess differential expression between any two groups of samples as defined by the user if you provide replication (n>1) in at least one group. You can subset the control group into subgroups and change the design accordingly, but it needs replicates.