Software and Code
- Distill, from Gianluca Pollastri’s group: http://distill.ucd.ie/distill/
- GEVA Application, from Michael O’Neill’s group: http://ncra.ucd.ie/Site/installgeva.html
- GEVA Source code, from the NCRA: http://code.google.com/p/geva/
- Dynamic Community Finding (Clique): http://cliquecluster.org/dynamic
- MOSES (Clique): http://www.cliquecluster.org/moses
- RProteinInteraction (Clique): http://cliquecluster.org/content/rproteininteraction-0
- Bioware : A suite of tools for the analysis of functional peptides: http://bioware.ucd.ie
- EpiC : A resource for functional and antigenic prediction of proteins: http://bioware.ucd.ie/epic/
- TextLuas (Clique) : Tools for tracking and visualizing document and term clusters in dynamic text data: http://mlg.ucd.ie/textluas
- Epistatic MAP Imputation (Clique) : Python code for the imputation and prediction of quantitative genetic interactions: http://cliquecluster.org/content/epistatic-map-imputation
- Ensemble NMF (Clique) : Software tools for aggregating and exploring a diverse collection of matrix factorizations to produce a superior clustering, which takes the form of an overlapping hierarchy of clusters: http://mlg.ucd.ie/nmf
- PICA (Clique) : Java-based software implementing a data integration approach for performing multi-view clustering in domains where two or more related datasets are available: http://mlg.ucd.ie/pica
- GCE (Clique) : C++ implementation of the Greedy Clique Expansion algorithm for detecting communities. The algorithm is especially designed for graphs in which most nodes belong to many communities: https://sites.google.com/site/greedycliqueexpansion/
- Group betweenness for JUNG (Java Universal Network/Graph Framework) : Implementation of the successive group betweenness algorithm by Puzis et. al (2007): 'Fast algorithm for successive computation of group betweenness centrality': http://sourceforge.net/tracker/?func=detail&atid=539121&aid=3174190&group_id=73840