MonkeyLB/mTDR: Comprehensively evaluate the reproducibility of chromatin profiling sequencing data

Enrichment-based chromatin profiling sequencing experiments have become essential tools to investigate the functional roles of genomic regions. Measuring reproducibility is central to the data quality control, and critical to ensure thecredibility of scientific discoveries. Evaluating the reproducibility of enrichment-based sequencing data is complicated by the variation of enrichment characteristics and the heterogeneous correlation structure between replicated samples. We present a model-based method to comprehensively assess the reproducibility between replicated samples. The method only requires minimum preprocessing of raw data and does not rely on peak calling. Thus it involves less information loss than the peak level reproducibility measure. The model is designed to assess three aspects of the data reproducibility ? the dependence between the enriched signals, the bulk correlation across whole range of signal values, and the degree of lack of enrichment. By the combination of the three quantities, our model is flexible to assess the reproducibility of data with different signal types (i.e., narrow-peak, broad-peak) and enrichment levels. We demonstrate that our method is also more accurate than the other existing measures.

install.packages("remotes")
remotes::install_github("MonkeyLB/mTDR")