The R Journal: article published in 2019, volume 11:1

Integration of networks and pathways with StarBioTrek package
Claudia Cava and Isabella Castiglioni , The R Journal (2019) 11:1, pages 310-322.

Abstract High-throughput genomic technologies bring to light a comprehensive hallmark of molecular changes of a disease. It is increasingly evident that genes are not isolated from each other and the identification of a gene signature can only partially elucidate the de-regulated biological functions in a disease. The comprehension of how groups of genes (pathways) are related to each other (pathway cross talk) could explain biological mechanisms causing diseases. Biological pathways are important tools to identify gene interactions and decrease the large number of genes to be studied by partitioning them into smaller groups. Furthermore, recent scientific studies have demonstrated that an integration of pathways and networks, instead of a single component of the pathway or a single network, could lead to a deeper understanding of the pathology. StarBioTrek is an R package for the integration of biological pathways and networks which provides a series of functions to support the user in their analyses. In particular, it implements algorithms to identify pathways cross-talk networks and gene network drivers in pathways. It is available as open source and open development software in the Bioconductor platform.

Received: 2018-05-01; online 2019-08-17, supplementary material, (1.2 KiB)
CRAN packages: XGR, qgraph, GOplot
CRAN Task Views implied by cited CRAN packages: Psychometrics
Bioconductor packages: NetPathMiner, ToPASeq, StarBioTrek, graphite

This article and supplementary materials are licensed under a Creative Commons Attribution 4.0 International license.

@article{RJ-2019-025,
  author = {Claudia Cava and Isabella Castiglioni},
  title = {{Integration of networks and pathways with StarBioTrek
          package}},
  year = {2019},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2019-025},
  url = {https://doi.org/10.32614/RJ-2019-025},
  pages = {310--322},
  volume = {11},
  number = {1}
}