Software Released at Virginia Tech

[Link to Murali Group Software]
  • PathLinker: Automated Reconstruction of Signaling Networks. Mentored student: Nick Sharp (undergraduate). Coming soon.
  • halp: Hypergraph Algorithms Package. Software that provides both a directed and an undirected hypergraph implementation as well as several important algorithms that operate on these hypergraphs. Mentored student: Brendan Avent (undergraduate). [GitHub] [PyPI]
  • GraphSpace: Sharing and Collaborating through Networks on the Web. Interactive graph visualization software designed for interdisciplinary collaborations. Mentored students: Craig Estep (graduate), Jaeil Yi (undergraduate), Divit Singh (graduate). [Create an Account] [View Public Graphs]
  • ASH: Active Sub-Hypergraphs. This software formulates the Active Sub-Hypergraphs problem as an integer linear program (ILP) and solves it using CPLEX. It was designed to identify active components of signaling pathways when they are represented as signaling hypergraphs. Mentored student: Amy Olex (graduate). [README] [tgz]

Software Released at Brown University

[Link to Raphael Group software]
  • MultiBreak-SV. Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms. [GitHub]
  • NBC: Neighborhood Breakpoint Conservation. NBC finds recurrent rearrangement breakpoints in DNA copy number data. [README] [tgz]
  • Gremlin: Genome Rearrangement Explorer with Multi-Scale, Linked Interactions. This is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes. [Gremlin Overview] [Interaction Guide] [Demo Gremlin Here]
  • MoDL: Motif Description Length. MoDL finds mutliple motifs in a set of phosphorylated peptides. [README] [tgz]