HiFive: a Tool Suite for Easy and Efficient HiC and 5C Data Analysis

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2015 Oct 27

PMID 26498826

Citations 31

Authors

Michael Eg Sauria

Jennifer E Phillips-Cremins

Victor G Corces

James Taylor

Affiliations

Soon will be listed here.

Abstract

The chromatin interaction assays 5C and HiC have advanced our understanding of genomic spatial organization, but analysis approaches for these data are limited by usability and flexibility. The HiFive tool suite provides efficient data handling and a variety of normalization approaches for easy, fast analysis and method comparison. Integration of MPI-based parallelization allows scalability and rapid processing time. In addition to single-command analysis of an entire experiment from mapped reads to interaction values, HiFive has been integrated into the open-source, web-based platform Galaxy to connect users with computational resources and a graphical interface. HiFive is open-source software available from http://taylorlab.org/software/hifive/ .

Citing Articles

DFHiC: a dilated full convolution model to enhance the resolution of Hi-C data.

Wang B, Liu K, Li Y, Wang J Bioinformatics. 2023; 39(5).

PMID: 37084258 PMC: 10166584. DOI: 10.1093/bioinformatics/btad211.

HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases.

Kobets V, Ulianov S, Galitsyna A, Doronin S, Mikhaleva E, Gelfand M Brief Bioinform. 2023; 24(2).

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Molecular and computational approaches to map regulatory elements in 3D chromatin structure.

Lee B, Rhie S Epigenetics Chromatin. 2021; 14(1):14.

PMID: 33741028 PMC: 7980343. DOI: 10.1186/s13072-021-00390-y.

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.

Kruse K, Hug C, Vaquerizas J Genome Biol. 2020; 21(1):303.

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Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.

Bulathsinghalage C, Liu L BMC Bioinformatics. 2020; 21(Suppl 14):369.

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