Do you know if it is possible to include samples for which I only have the counts to perform the analysis? Either adding to the pipeline or in R studio once the pipeline has been completed.

Are you talking about splicing analysis? What kind of counts do you have, i.e. what are the units being counted -- genes, transcripts, exons?

Yes, and I have exon counts.

You can probably run DEXSeq. I think you'll need to know what GTF/GFF the counts come from. It will give you (parts of) exons that are differentially expressed. Unfortunately without BAM files you will not able to check any result for artifacts, but it's better than nothing.

Thank you! I will try