C3D specifications


Unique identifier OMICS_21927
Name C3D
Alternative name Cross Cell-type Correlation based on DNA accessibility
Software type Application/Script
Interface Command line interface
Restrictions to use None
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.
Input format GED+BEDGRAPH
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.
Operating system Unix/Linux
Programming languages R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1
Stability Stable
Requirements bedtools, GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut
Maintained Yes



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  • person_outline Mathieu Lupien <>
  • person_outline Tahmid Mehdi <>

Publication for Cross Cell-type Correlation based on DNA accessibility

C3D institution(s)
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
C3D 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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