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Cross Cell-type Correlation based on DNA accessibility C3D


Allows prediction of chromatin interactions using an unsupervised algorithm. C3D computes correlations between genomic measurements to predict chromatin interactions between genomic regions of interest. These genomic measurements can be DNase-seq or ATAC-seq signal intensities. The software can control for false positives if adequate databases and correlation thresholds are applied.

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C3D classification

C3D specifications

Software type:
Restrictions to use:
Input format:
Operating system:
GNU General Public License version 3.0
bedtools, GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut
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:

C3D distribution


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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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