HiC-bench specifications


Unique identifier OMICS_13577
Name HiC-bench
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Alignment of reads
Input format FASTQ
Output data Annotation of specific interactions, their visualization, enrichment analysis
Operating system Unix/Linux
Programming languages R
License MIT License
Computer skills Advanced
Version 0.1
Stability Stable
Bowtie2 aligner, Python, Numpy, Scipy, Matplotlib, R::lattice, RColorBrewer, corrplot, reshape, gplots, preprocessCore, zoo, reshape2, plotrix, pastecs, boot, optparse, ggplot2, igraph, Matrix, MASS, flsa, VennDiagram, futile.logger, plyr
Maintained Yes




No version available



  • person_outline Aristotelis Tsirigos

Publication for HiC-bench

HiC-bench citations


Stratification of TAD boundaries reveals preferential insulation of super enhancers by strong boundaries

Nat Commun
PMCID: 5803259
PMID: 29416042
DOI: 10.1038/s41467-018-03017-1

[…] All ChIP-seq data were uniformly processed using the HiC-bench platform. Raw sequencing files were aligned using Bowtie2 version 2.3.1 with standard parameters. Only uniquely mapped reads were selected for downstream analysis. PCR duplicates were remove […]


lncRNA screen: an interactive platform for computationally screening long non coding RNAs in large genomics datasets

BMC Genomics
PMCID: 5458484
PMID: 28583068
DOI: 10.1186/s12864-017-3817-0

[…] g expression profile and H3K4me3, H3K27ac and H3K4me1 histone mark occupancy. The numbers of elements in each category for each cell type are included in Table . Hi-C analysis was performed using our HiC-bench pipeline []. HiC-bench automatically produces various plots to help the user assess the quality of the data as well as compare different samples. Paired-end reads were mapped to the referenc […]

HiC-bench institution(s)
Department of Pathology, NYU School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, USA; Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, NY, USA; Genome Technology Center, Office of Science & Research, NYU School of Medicine, NY, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
HiC-bench funding source(s)
The study was supported by a Research Scholar Grant, RSG-15-189-01 - RMC from the American Cancer Society and a Leukemia & Lymphoma Society New Idea Award, 8007-17.

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