Software

Software Released at Reed College

Pathway Connectivity. Data and source code for (nearly) all figures and experiments from Hypergraph-based connectivity measures for signaling pathway topologies. Also makes use of halp. GitHub

Localized PathLinker (LocPL). LocPL is a compartment-constrained pathway reconstruction method that refines PathLinker paths by protein localization. GitHub

Motility-Related Schizophrenia Gene Predictor. SZ Gene Predictor includes code to identify genes that are functionally associated with a disease (e.g. schizophrenia) and a phenotype (e.g. cell motility). GitHub

Software Released at Virginia Tech

Murali Group Software

PathLinker. Algorithm that computes the k shortest loopless paths in a weighted directed network, originally developed to reconstruct human signaling pathways. GitHub

halp: Hypergraph Algorithms Package. Software that provides both directed and undirected hypergraph implementations and algorithms. GitHub PyPI

GraphSpace: Sharing and Collaborating through Networks on the Web. Interactive network visualization software designed for interdisciplinary collaborations. GitHub View Public Graphs

Software Released at Brown University

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.

Gremlin: Genome Rearrangement Explorer with Multi-Scale, Linked Interactions. Interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.

MoDL: Motif Description Length. MoDL finds mutliple motifs in a set of phosphorylated peptides using an description length, a concept borrowed from information theory.

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Contact

Biology Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

Email icon aritz-at-reed-dot-edu

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