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Citations per year

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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


No version available

Documentation


Maintainer


  • person_outline Juli Petereit

Publication for petal

petal citations

 (4)
library_books

Discovering Condition Specific Gene Co Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study

2017
Sci Rep
PMCID: 5561081
PMID: 28819158
DOI: 10.1038/s41598-017-09094-4

[…] n modules”. A variety of software tools exists for GCN construction with each employing different approaches for identifying co-expression. These include tools such as, WGCNA, CLR, MRNET, RMTGeneNet, petal and FastGCN. WGCNA is the most popular network construction tool in terms of citations.Some studies use hundreds to thousands of samples to create a GCN–. The use of hundreds of samples for GCN […]

library_books

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

2017
BMC Plant Biol
PMCID: 5450095
PMID: 28558655
DOI: 10.1186/s12870-017-1043-1

[…] CNA (Weighted Gene Co-expression Network Analysis) is one approach that was effectively used to identify highly connected hubs in gene subnetworks for Arabidopsis [, ] and Vitis []. Another approach, petal [], was developed recently to provide a truly scale-free and small-world network model for large-scale Omics analyses. A common set of transcriptional changes occurring in the late ripening stag […]

library_books

Comparative transcriptomics of mountain pine beetle pheromone biosynthetic tissues and functional analysis of CYP6DE3

2017
BMC Genomics
PMCID: 5397757
PMID: 28427347
DOI: 10.1186/s12864-017-3696-4

[…] ertheless, mevalonate pathway enzymes are more predominantly represented in fed males compared to females, consistent with frontalin production (Fig. ). In parallel, co-expression network analysis by petal using a Spearman Correlation Coefficient and similarity threshold of 0.808 also isolated candidate genes. As these expression data were not normally distributed, the Spearman Correlation Coeffic […]

library_books

The tomato floral homeotic protein FBP1 like gene, SlGLO1, plays key roles in petal and stamen development

2016
Sci Rep
PMCID: 4740859
PMID: 26842499
DOI: 10.1038/srep20454

[…] organs in tomato showed that the SlGLO1 mRNA was highly accumulated in petals and stamens (), which was coincidence with the study of Geuten and Irish where they show SlGLO1 is expressed in incipient petal and stamen primordia in early developmental stages by in situ hybridization. These results indicate that SlGLO1 may have a specialized function in flower development process. […]


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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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