Processing

• Quality control, trimming and alignment or pseudoalignment
• Normalisation choices and their downstream consequences
• Batch correction methods and the risk of removing real signal

Discovery

• Differential expression with appropriate dispersion modelling
• Multiple testing correction and effect-size reporting
• Pathway and gene-set enrichment, and the interpretive traps in it

Integration

• Integrating transcriptomic, proteomic and metabolomic layers
• Co-expression and regulatory network inference, and its weak identifiability
• Prioritising candidates for experimental follow-up

Validation

• Independent cohort validation and reproducibility expectations
• Designing the wet-lab experiment that would falsify the finding
• Reporting standards and data deposition for omics publications