Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

Biologically-Related Apriori Network Enhancement with graph Cuts BRANE Cut


A weighted graph thresholding method. Using biologically sound penalties and data-driven parameters, BRANE Cut improves three state-of-the-art gene regulatory network (GRN) inference methods. The proposed method generalizes standard regulatory network inference by incorporating additional terms with biological interpretation. Since their regularization parameters are estimated from gene set cardinality, it can be applied to various transcriptomic data. The computation time of our method is negligible in comparison with other model-based approaches with inference improvements. It can be used as a generic GRN post-processing with any input weights and supplementary information on transcription factors.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

0 user reviews

No review has been posted.

BRANE Cut forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

BRANE Cut classification

BRANE Cut specifications

Software type:
Restrictions to use:
Programming languages:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:

BRANE Cut distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

BRANE Cut support


  • Aurélie Pirayre <>


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



IFP Energies Nouvelles, Rueil-Malmaison, France; Université Paris-Est, Laboratoire d’Informatique Gaspard-Monge, Marne-la-Vallée, France

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.