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FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays important roles in genome function. Frequently interacting regions (FIREs) are more informative for tissue-specific chromatin interactions than the well-established Hi-C readouts, such as A/B compartments, topologically associating domains (TADs) and chromatin loops. FIREcaller is a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrix as input, performs within-sample and cross-sample normaliza-tion via HiCNormCis and quantile normalization respectively, and outputs FIRE scores, FIREs and super-FIREs. The current version is a pre-release. For details, please refer to our tutorial.

Comments and suggestions are welcome, please e-mail Cheynna Crowley at, Ming Hu at or Yun Li at