scDenorm: a denormalisation tool for integrating single-cell transcriptomics data

Integrating single-cell omics data at an atlas scale enhances our understanding of cell types and disease mechanisms. However, the integration of data processed by different normalisation methods can lead to biases, such as unexpected batch effects and gene expression distortion, leading to misinterpretations in downstream analysis. To address these challenges, we present scDenorm, an algorithm that reverts normalised single-cell omics data to raw counts, preserving the integrity of the original measurements and ensuring consistent data processing during integration. We evaluated scDenorm’s performance on large-scale datasets and benchmarked its impact on data integration and downstream analysis across three datasets.