CovNorm: An R package for coverage based normalization of Hi-C and capture Hi-C data.

ABSTRACT: 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 enha

SUBMITTER: Kim K 

PROVIDER: S-EPMC8188117 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature