Tools for Normalizing and Comparing ChIP-seq Samples R package MAnorm2 version 1.2.2 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. Software Depends: R (>= 3.5.0) Imports: stats, graphics, methods, locfit (>= 1.5.9), scales (>= 0.3.0), statmod (>= 1.4.34) Suggests: gplots (>= 3.0.1), DescTools (>= 0.99.24), knitr, rmarkdown Shiqi Tu <tushiqi@picb.ac.cn> Comprehensive R Archive Network (CRAN) Shiqi Tu [aut, cre] (ORCID: <https://orcid.org/0000-0003-3534-5714>) GPL-3 2022-10-28 application/tgz https://CRAN.R-project.org/package=MAnorm2 doi:10.32614/CRAN.package.MAnorm2