Integration of networks and pathways with StarBioTrek package

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.

Claudia Cava , Isabella Castiglioni

Supplementary materials

Supplementary materials are available in addition to this article. It can be downloaded at

CRAN packages used

XGR, qgraph, GOplot

CRAN Task Views implied by cited packages


Bioconductor packages used

NetPathMiner, ToPASeq, StarBioTrek, graphite


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".


For attribution, please cite this work as

Cava & Castiglioni, "The R Journal: Integration of networks and pathways with StarBioTrek package", The R Journal, 2019

BibTeX citation

  author = {Cava, Claudia and Castiglioni, Isabella},
  title = {The R Journal: Integration of networks and pathways with StarBioTrek package},
  journal = {The R Journal},
  year = {2019},
  note = {},
  doi = {10.32614/RJ-2019-025},
  volume = {11},
  issue = {1},
  issn = {2073-4859},
  pages = {310-322}