Implementing BigClam in cicero

[Matt R]

Hi Hannah,

Huge fan of Cicero and the implementation of Louvain graph based clustering of regulatory elements!

Louvain is a 'hard' partitioning algorithm, meaning that regulatory elements cannot belong to more than one cluster or CCAN.

Since in real biology, regulatory elements could in fact participate in multiple CCANs or regulatory networks, would it be possible to implement a soft-partitioning method, such as Big Clam?

Here is the paper:

https://cs.stanford.edu/people/jure/pubs/bigclam-wsdm13.pdf

If you want to follow up for further collaboration or questions, please feel free to reach out through Gmail or contact info below:

Best,

Matt Regner, PhD Student

Twitter: @RegnerMJ

Github: RegnerM2015

[hpl...@gmail.com]

Hi Matt,

Thanks for reaching out. That seems like a good idea, but it's unlikely I'll have bandwidth to add it in the near future. I'm very open to pull requests though it you'd like to attempt an implementation!

Best,

Hannah

[Matt R]

Hi Hannah!

Thanks for getting back to me!

I feel your pains with limited bandwidths, but I would like to potentially propose a pull request! If I decide to pursue this implementation, I will reach out to in a few months from now.

Best,

Matt