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Preprint

HiCRep analysis

SS Sarah G Swygert
TT Toshio Tsukiyama

Last updated date: Aug 2, 2022 Views: 527 Forks: 0

original An abbreviated version of this protocol was published in eLife in Nov, 2021
Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells
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HiCRep code and instructions for implementing in Python are available here:

 

https://github.com/dejunlin/hicrep

 

Please also see the referenced publication:

 

Dejun Lin, Justin Sanders, William Stafford Noble, HiCRep.py: fast comparison of Hi-C contact matrices in Python, Bioinformatics, Volume 37, Issue 18, 15 September 2021, Pages 2996–2997, https://doi.org/10.1093/bioinformatics/btab097

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Swygert, S and Tsukiyama, T(2022). HiCRep analysis. Bio-protocol Preprint. bio-protocol.org/prep1840.
  2. Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P., Hunt, D. R., Kao, C., Schlick, T., Noble, W. S. and Tsukiyama, T.(2021). Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife. DOI: 10.7554/eLife.72062

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