PopNet specifications


Unique identifier OMICS_30107
Name PopNet
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A matrix of SNPs.
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Numpy, Matplotlib, MCL
Maintained Yes




No version available


  • person_outline John Parkinson
  • person_outline Michael Grigg

Publication for PopNet

PopNet citation


Nitrogen driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation

BMC Plant Biol
PMCID: 4302602
PMID: 25547614
DOI: 10.1186/s12870-014-0391-3
call_split See protocol

[…] an and SD for 100 bootstraps of the input set (duplicates allowed) and the p of the hypergeometric distribution []. Gene coexpression relationships were calculated for the DEGs with the Analysis Tool PopNet in Popgenie v3.0 ( with a display threshold of 7 and an expand threshold of 3. The coexpression analysis was based on microarray data from 21 experiments (GSE12152, GSE1310 […]

PopNet institution(s)
Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada; Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD, USA; Departments of Computer Science and Molecular Genetics, University of Toronto, Toronto, ON, Canada
PopNet funding source(s)
Supported by the Canadian Institute for Health Research (CIHR-MOP 84556), the Natural Sciences and Engineering Research Council of Canada (RGPIN-2014-06664) and the Intramural Research Program of the NIH and NIAID and by a scholar of the Canadian Institute for Advanced Research (CIFAR) Integrated Microbial Biodiversity Program.

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