HiC-bench specifications

Unique identifier:
OMICS_13577
Interface:
Command line interface
Input data:
Alignment of reads
Output data:
Annotation of specific interactions, their visualization, enrichment analysis
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTQ
Operating system:
Unix/Linux
License:
MIT License
Version:
0.1
Requirements:
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

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HiC-bench distribution

download

HiC-bench support

Documentation

Maintainer

  • Aristotelis Tsirigos <>

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Credits

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Publications

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

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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