Batch characterisation/simulation

Batch characterisation and simulation of realistic batch effects

To create realistic benchmark tasks it’s important to understand main characteristics of real data batch effects. This is why we characterised batch effects from 9 different real data batch scenarios with focus on batch strength, celltype-specificity and batch type. We used these insights to (simulate realistic batch effects)[https://almutlue.github.io/batch_snakemake/simulation_index.html], with celltype specific logFC distributions, while retaining covariance structure between them.