Protocols

PopNet specifications

Information


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
Requirements
Numpy, Matplotlib, MCL
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline John Parkinson
  • person_outline Michael Grigg

Publication for PopNet

PopNet citation

call_split

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

2014
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 (http://popgenie.org/) 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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