文章基本信息

标题：covNorm: An R package for coverage based normalization of Hi-C and capture Hi-C data
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作者：Kyukwang Kim ; Inkyung Jung
期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2021
卷号：19
页码：3149-3159
DOI：10.1016/j.csbj.2021.05.041
出版社：Computational and Structural Biotechnology Journal
摘要：Hi-C and capture Hi-C have greatly advanced our understanding of the principles of higher-order chromatin structure. In line with the evolution of the Hi-C protocols, there is a demand for an advanced computational method that can be applied to the various forms of Hi-C protocols and effectively remove innate biases. To resolve this issue, we developed an implicit normalization method named “covNorm” and implemented it as an R package. The proposed method can perform a complete procedure of data processing for Hi-C and its variants. Starting from the negative binomial model-based normalization for DNA fragment coverages, removal of genomic distance-dependent background and calling of the significant interactions can be applied sequentially. The performance evaluation of covNorm showed enhanced or similar reproducibility in terms of HiC-spector score, correlation of compartment A/B profiles, and detection of reproducible significant long-range chromatin contacts compared to baseline methods in the benchmark datasets. The developed method is powerful in terms of effective normalization of Hi-C and capture Hi-C data, detection of long-range chromatin contacts, and readily extendibility to the other derivative Hi-C protocols. The covNorm R package is freely available at GitHub: https://github.com/kaistcbfg/covNormRpkg .
关键词：Hi-C ; Promoter capture Hi-C ; Higher-order chromatin structure ; Long-range chromatin contact ; Epigenetics