Timeline for factor interactions implementation

[victorsanchezarevalo]

Timeline for factor interactions implementation

Feature Request

I'm interested in using factor interactions in pydeseq2 for analyzing complex experimental designs with multiple variables.

Background

This is crucial for experiments with:

• Treatment × time interactions
• Genotype × condition interactions
• Multiple factorial designs

Current Status Question

Could the maintainers provide information about:

1. What's the expected timeline for this feature?

Use Case

My specific use case involves analyzing RNA-seq data with a 2×3 factorial design (2 genotypes × 3 time points), where I need to identify genes where the treatment response differs between genotypes.

Thank you for all the effort you have put into developing pydeseq2!

[BorisMuzellec]

Hi @victorsanchezarevalo,

Genotype × condition interactions and multiple factorial designs are already supported, e.g. you can use designs like design="~condition + treatment" or design="~condition:treatment" (or any Wilkinson formula supported by formulaic and formulaic-contrasts)

Time interactions are not supported yet. Although I'm happy to help anyone willing to give a go at this I don't have any bandwidth to work on this myself.