hicrep
Bioc removedMeasuring the reproducibility of Hi-C data
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Entered 3.5 · Apr 25, 2017
Removed after 3.12 · Oct 28, 2020
Description
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwiseß differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth. Compared to existing approaches, it consistently shows higher accuracy in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages than existing approaches. This R package `hicrep` implements our approach.
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citation("hicrep")Bioconductor packages have no CRAN DOI. The package landing page is https://bioconductor.org/packages/hicrep.
BibTeX, derived from DESCRIPTION
@Manual{hicrep,
title = {hicrep: Measuring the reproducibility of Hi-C data},
author = {Yang, Tao and Song, Fan},
year = {2020},
note = {R package version 1.14.0},
url = {https://bioconductor.org/packages/hicrep}
}Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.
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BibTeX
@misc{robservatoryhicrep,
author = {Balamuta, James Joseph},
title = {{R} {Observatory}: Metrics for {hicrep} version 1.14.0},
year = {2026},
publisher = {HJJB, LLC},
url = {https://r-observatory.thecoatlessprofessor.com/bioc/hicrep},
note = {Data set. Data release v2026-08-05}
}APA
Balamuta, J. J. (2026). R Observatory: Metrics for hicrep version 1.14.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/bioc/hicrepRIS
TY - DATA
AU - Balamuta, James Joseph
TI - R Observatory: Metrics for hicrep version 1.14.0
PY - 2026
PB - HJJB, LLC
N1 - Data release v2026-08-05
UR - https://r-observatory.thecoatlessprofessor.com/bioc/hicrep
ER - In prose
These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/bioc/hicrep.Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.