C3D specifications

Unique identifier:
Software type:
Restrictions to use:
Input format:
Operating system:
GNU General Public License version 3.0
bedtools, GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut
Cross Cell-type Correlation based on DNA accessibility
Command line interface
Input data:
A file of accessible genomic regions, a file of potential chromatin loop anchors (for example, promoters of genes you are interested in) and files of DNase I hypersensitivity signals for each biological sample you want to calculate correlations across.
Output data:
Genomic coordinates of open region in an anchor, genomic coordinates of open region that is distal to an anchor, correlation score between, ID of anchor that COORD_1 overlaps, P-value from association test between COORD_1 and COORD_2 and adusted p-value after performing multiple test correction.
Programming languages:
R, Shell (Bash)
Computer skills:


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C3D distribution


C3D support


  • Mathieu Lupien <>
  • Tahmid Mehdi <>


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Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada

Funding source(s)

Supported by Prostate Cancer Canada and is proudly funded by the Movember Foundation (grant #RS2014-04 ), with the additional support of the Canadian Cancer Society and the Princess Margaret Cancer Foundation, an Investigator Award from the Ontario Institute for Cancer Research; a Canadian Institutes of Health Research (CIHR) New Investigator Award; a Movember Rising Star Award from Prostate Cancer Canada and a CIHR Fellowship (MFE 338954) and a Knudson and CIHR postdoctoral fellowship recipient.

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