Software

We develop algorithms and software to facilitate the analysis and interpretation of large-scale genomic datasets. Source code is made freely available, mostly through GitHub. Follow any of the links below for more information and please let us know if any of these tools helped you in your research.

Network inference

Statistics

  • Bayonet – Matlab implementation of an analytic solution and stationary phase approximation for the Bayesian lasso and elastic net. [homepage] [paper]
  • Lassopv – R package for obtaining p-values in Lasso regression. [homepage][paper]
  • Glmnat – Matlab implementation of the natural coordinate descent algorithm for L1-penalised regression in generalized linear models. [homepage] [paper]
  • kruX – A Matlab/R/Python tool for simultaneously performing millions of non-parametric ANOVA (Kruskal-Wallis) tests using matrix-multiplication methods. [homepage] [paper]

Network topology and motif analysis

  • SCHype – A Java command line tool for spectral clustering in hypergraphs. [homepage] [paper]
  • ISMA – The Index-based Subgraph Matching Algorithm. [homepage] [paper]
  • Network Motif Clustering Toolbox – a Matlab toolbox for clustering topological motifs in integrated networks. [homepage] [paper]
  • CyClus3D – a Cytoscape plugin for clustering network motifs in integrated networks. [homepage] [paper]
  • Pathicular – a Cytoscape plugin for identifying regulatory path motifs in integrated networks. [homepage] [paper]
  • MatrixClust – a Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network. [homepage] [paper] [paper]

Resources

  • DHSgen – A list of high-confidence predicted interactions between regulatory genome regions and their target genes. [homepage] [paper].
  • RNA regulon-omics – A portal for molecular biologists who wish to design detailed hypotheses from a large-scale, top-down analysis of posttranscriptional regulation in yeast. [homepage] [paper]

Statistical physics

  • D-MiRaGe – a Matlab toolbox for performing ground state and time-dependent Density Matrix Renormalization Group computations for one-dimensional quantum spin systems which need not be translation invariant. [homepage] [paper] [paper]
  • DNAmelt – a Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model. [homepage] [paper]