petal statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene co-expression prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

petal specifications

Information


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

Versioning


Add your version

Documentation


Maintainer


  • person_outline Juli Petereit <>

Publication for petal

petal in publication

PMCID: 5450095
PMID: 28558655
DOI: 10.1186/s12870-017-1043-1

[…] modules or more and six higher order gene subnetworks. some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. the petal r package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. a subnetwork of 216 genes with the highest connectivity […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

petal reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review petal