Software
Software Released at Reed College
SPRAS. Source code for the Signaling Pathway Reconstruction Analysis Streamliner (SPRAS), a dockerized framework to easily run different pathway reconstruction algorithms.
Graphery. Source code for the interactive biological network tutorial, with ability to start a local server. See the tutorial website for our hosted version.
Growing DAGS. Code and datasets to iteratively grow directed acyclic graphs for signaling pathway reconstruction.
Pathway Reconciliation. Code and datasets that use network topologies (graphlets) to reconcile signaling pathways across pathway databases.
PRoBERTa. Code and datasets related to our work on protein family classification and interaction prediction tasks using transformer neural networks.
PRAUG. Code and datasets from PRAUG: the Pathway Reconstruction AUGmenter.
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.
Localized PathLinker (LocPL). LocPL is a compartment-constrained pathway reconstruction method that refines PathLinker paths by protein localization.
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).
Software Released at Virginia Tech
PathLinker. Algorithm that computes the k shortest loopless paths in a weighted directed network, originally developed to reconstruct human signaling pathways.
halp: Hypergraph Algorithms Package. Software that provides both directed and undirected hypergraph implementations and algorithms. 
GraphSpace: Sharing and Collaborating through Networks on the Web. Interactive network visualization software designed for interdisciplinary collaborations. View Public Graphs
Software Released at Brown University
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.
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.
aritz-at-reed-dot-edu
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