petal specifications


Unique identifier OMICS_12597
Name petal
Software type Package/Module
Interface Command line interface
Restrictions to use None
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.
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.
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements igraph
Maintained Yes


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  • person_outline Juli Petereit <>

Publication for petal

petal institution(s)
University of Nevada, Reno, Reno, NV, USA
petal 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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