petal specifications

Unique identifier:
OMICS_12597
Interface:
Command line interface
Input data:
The user supplies the expression data file to petal. In addition, there are four optional steps: the selection of an association measure, user-specified thresholds (for the advanced user), the upload of a list of genes which are of particular interest to the researcher, and a gene annotation file. Additionally, the user has the option to evaluate their data distribution by using the function graphHistQQFromFile before constructing a network model.
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Stability:
Stable
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Output data:
Upon completion, petal’s accessible files include: general information file (.txt), network file (.txt), adjacency matrices (.RData), two topology tables (.txt), vicinity network files (.txt), and the expression profiles (.tiff) of each vicinity network. The network file can be directly uploaded into Cytoscape.
Programming languages:
R
Computer skills:
Advanced
Requirements:
igraph

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petal support

Documentation

Maintainer

  • Juli Petereit <>

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Publications

Institution(s)

University of Nevada, Reno, Reno, NV, USA

Funding source(s)

This work is based upon work supported by the Department of Energy (DOE), Office of Science, Genomic Science Program under Award Number DE-SC0008834. This work was also made possible by a grant from the National Institute of General Medical Sciences (P20GM103440) from the National Institutes of Health through its support of the Nevada Center for Bioinformatics.

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