R package associated with the CeDAR: incorporating cell type hierarchy improves cell type specific differential analyses in bulk omics data.

This is the R package associated with the work "CeDAR: incorporating cell type hierarchy improves cell type specific differential analyses in bulk omics data". The function cedar() implemented in this R package (TOAST) is corresponding to the method described in the work. Motivation: Identifying cell type specific differential expression/methylations (csDE/csDM) from bulk data is a popular way to study cell type specific activities. However, existing methods have poor performance in small proportion cell types and the only way to improve the performance is to increase sample size. Result: In real data exploration, we found that differential expression/methylation (DE/DM) states among cell types are correlated. We designed a novel hierarchical model which captures such correlations by incorporating cell type hierarchy (CeDAR). Both simulation and real data analysis demonstrate that the new method can improve cell type specific differential analysis on bulk omics data, especially in small proportion cell types