C3D specifications

Unique identifier:
OMICS_21927
Software type:
Application/Script
Restrictions to use:
None
Input format:
GED+BEDGRAPH
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
0.1
Requirements:
bedtools, GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut
Name:
Cross Cell-type Correlation based on DNA accessibility
Interface:
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:
Advanced
Stability:
Stable
Maintained:
Yes

versioning

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C3D distribution

download

C3D support

Maintainers

  • Mathieu Lupien <>
  • Tahmid Mehdi <>

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Publications

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

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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