Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 65,690 bioRxiv papers from 290,986 authors.

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

By Cheynna Crowley, Yuchen Yang, Yunjiang Qiu, Benxia Hu, Hyejung Won, Bing Ren, Ming Hu, Yun Li

Posted 29 Apr 2019
bioRxiv DOI: 10.1101/619288

Motivation: Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an important role in genome function. Well-established Hi-C readouts include A/B compartments, topologically associating domains (TADs) and chromatin loops. We have recently proposed another readout: frequently interacting regions (FIREs) and discovered them to be informative about tissue-specific gene expression. However, computational tools for detecting FIREs from Hi-C data are still lacking. Results: In this work, we have developed FIREcaller, 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 normalization via HiCNormCis and quantile normalization respectively, and outputs continuous FIRE scores, dichotomous FIREs and super-FIREs. Availability and implementation: The FIREcaller package is implemented in R, freely available at https://yunliweb.its.unc.edu/FIREcaller.

Download data

  • Downloaded 218 times
  • Download rankings, all-time:
    • Site-wide: 44,481 out of 65,690
    • In bioinformatics: 5,081 out of 6,504
  • Year to date:
    • Site-wide: 21,091 out of 65,690
  • Since beginning of last month:
    • Site-wide: 27,458 out of 65,690

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News