Arboretum-HiC specifications


Unique identifier OMICS_14590
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data A different Hi-C data sets, a tree describing the hierarchical relationship between the data sets, the number of clusters k, and a mapping of regions between the different data sets
Output data The cluster assignments of regions in each Hi-C data set
Operating system Unix/Linux
Programming languages MATLAB, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Sushmita Roy <>

Arboretum-HiC article

Arboretum-HiC institution(s)
Department of Computer Sciences, University of Wisconsin, Madison, WI, USA; La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
Arboretum-HiC funding source(s)
This work was supported by a Computing Research Association CIFellows award (National Science Foundation (NSF) award Computing Innovation Fellowship (CIF) 1136996), by the Institute Leadership Professorship Fund from La Jolla Institute for Allergy and Immunology, in part by National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Environmental Health Sciences (NIEHS), NINDS (National Institute of Neurological Disorders and Stroke), National Institute on Deafness and Other Communication Disorders (NIDCD), and NIAAA (National Institute on Alcohol Abuse and Alcoholism) of the National Institutes of Health (NIH) under award number U54AI117924, by an NSF Career award (NSF Division of Biological Infrastructure(DBI): 1350677) and a Sloan Foundation research fellowship.

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