DiffuPath

DiffuPath is an analytic tool for biological networks that connects the generic label propagation algorithms from DiffuPy to biological networks encoded in several formats such as Simple Interaction Format (SIF) or Biological Expression Language (BEL). For example, in the application scenario presented in the paper, we use three pathway databases (i.e., KEGG, Reactome and WikiPathways) and their integrated network retrieved from PathMe [1] to analyze three multi-omics datasets. However, other biological networks can be imported from the Bio2BEL ecosystem [2].

Installation is as easy as getting the code from PyPI with python3 -m pip install diffupath. See the installation documentation.

See also

Disclaimer

DiffuPath is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.

References

[1]Domingo-Fernandez, D., Mubeen, S., Marin-Llao, J., Hoyt, C., et al. Hofmann-Apitius, M. (2019). PathMe: Merging and exploring mechanistic pathway knowledge.. BMC Bioinformatics, 20:243.
[2]Hoyt, C. T., et al. (2019). Integration of Structured Biological Data Sources using Biological Expression Language. bioRxiv, 631812.