Feature Request: Expression Quantification Support (Isoform, Gene, TPM, DE)

[AR-Shicheng]

Description of feature

Hi team, thanks for the great work on nf-core/isoseq! I’m using v2.0.0 for Iso-Seq analysis and would love support or guidance for downstream expression quantification. Specifically:

Isoform-level expression: Read counts per isoform from TAMA or aligned FLNCs

Gene-level expression: Aggregated counts from isoforms

Normalized values: TPM or FPKM calculation

DE analysis: Integration with DESeq2 or similar for multi-condition comparisons

Are there any plans to support this, or existing best practices you recommend? Happy to test or contribute if helpful.

Thanks!