MAnorm2 - Tools for Normalizing and Comparing ChIP-seq Samples

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the premier technology for profiling genome-wide localization of chromatin-binding proteins, including transcription factors and histones with various modifications. This package provides a robust method for normalizing ChIP-seq signals across individual samples or groups of samples. It also designs a self-contained system of statistical models for calling differential ChIP-seq signals between two or more biological conditions as well as for calling hypervariable ChIP-seq signals across samples. Refer to Tu et al. (2021) <doi:10.1101/gr.262675.120> and Chen et al. (2022) <doi:10.1186/s13059-022-02627-9> for associated statistical details.