Michoel Group | Software

Our group develops algorithms and software to facilitate the analysis and interpretation of large-scale genomic datasets. 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 a 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]