PathLinker

PathLinker is a pathway reconstruction algorithm which links the sources and target of the input interactome with a k-shortest paths (implemented with Yen’s algorithm) to a pathway reconstruction context.

PathLinker takes one optional argument:

• k: The number of paths to find (k shortest paths).

Dataset Usage

PathLinker uses sources, targets, and edge weights. PathLinker uses edge direction information.

Implementation Details

Internally, PathLinker only takes in directed graphs. SPRAS will automatically convert edges to directed edges as necessary. For more information, see the section on algorithm directionality.

External links

• Source code: https://github.com/Murali-group/PathLinker

• Associated papers: https://doi.org/10.1038/npjsba.2016.2 and https://doi.org/10.1089/cmb.2012.0274.