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Software

Software and Libraries developed in our group

Cytoscape

Other links:

Proteomics

  • FragMixer software for automated phosphopeptide identification using multiple MS/MS fragmentation modes (paper)

Bioinformatics

  • Enrichment, a Python library to evaluate the over or under representation of occurrences in a list (such as pathways in a list of genes of interest.

  • SemanticDistance, a Python library to calculate a distance between terms in an ontology.

  • knn, a C implementation of the k-nearest neighbor classifier with enhanced support for gene expression data.

  • findGenes, a tool to find interactors in regulatory networks (implemented in C). Starting from a sets of seed genes the program searches, assesses and ranks candidate based on the observed strenght of statistical interactions between their expression pattern and those of the seed genes. While still an early prototype, the software already supports five different interaction measures. The prototype is available as a precompiled Linux 32-bit executable or as compressed source code in tar.gz or zip format. Please refer to the source package for the preliminary documentation. Note that the current version of the software requires installation of the GNU Scientific Library.

  • scoreKO, a Python program for regulatory pathway search and network induction.