Please see our GitHub organisation for active and recent software projects. This page lists older packages. We have released all software on this page under version 3 of the GNU General Public License. Many of these individual packages are available as part of the Biorithm software suite. For packages that are part of Biorithm, the links below take you to the documentation for each package.

• Network and Pathway Analysis
  • GraphSpace, a website for uploading, sharing, and collaborating with networks.
  • PathLinker, a path-based algorithm to reconstruct interactions in signaling pathways.
  • halp, a library of algorithms for directed and undirected hypergraphs.
  • XTalk, a path-based approach for detecting crosstalk between signaling pathways.
• Data-Driven Systems Biology
  • Concise, Functional Enrichment of Ranked Gene Lists, a method to compute a small set of non-redundant functions that annotated a ranked list of genes.
  • NetworkLego, find networks of molecular interactions activated in a cell state or in response to a particular perturbation or stimulus and compare and contrast these active networks to construct network legos, building blocks of the molecular interaction network.
  • Functional enrichment, different methods for computing which sets of pre-defined genes (e.g., biological pathways) are over-represented in another set of genes, e.g., differentially-expressed genes in a treatment-control study.
  • GraphHopper, a method for finding conserved protein interaction networks. This software is not part of Biorithm.
• Predicting Gene Function
  • GAIN, a system for whole-genome prediction of gene functions
• Gene Expression Analysis
  • xMotif, an algorithm for computing biclusters in gene expression data and (optionally) building nearest-neighbour sample classifiers based on these biclusters.
  • BiVoC, a system for automatic layout and visualisation of biclusters
• Data Mining
  • Bicluster mining in binary matrices, our implementation of a level-wise algorithm to find closed biclusters in binary matrices. This algorithm is similar to Apriori (it incrementally adds rows rather than columns), except that whenever it finds a new bicluster it immediately adds all possible rows that make the bicluster closed. The software outputs both the rows and columns of the biclusters it finds.
  • Truthiness mining, a method to find truth tables in binary and categorical matrices.