I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential expression of transcripts then performing some downstream manual analysis to find which of the differential transcripts belong to same gene. Or if there is any other R package that can perform DIE analysis by taking in salmon quant files directly.
I know DESeq2 is used for gene-level analysis, I am not sure if it can be extended to transcript level and if there are any underlying parameters I should take into consideration before performing such analysis.
Any advice will be highly appreciated.