Maastricht University, The Netherlands

Our Main Projects on Software Tools and Services

Data Analysis Pipelines

  • ArrayAnalysis: Quality Control, pre-processing, normalization and statistics of Affymetrix microarrays

Identifier Mapping

  • BridgeDb: database identifier mapping framework for bioinformatics applications
  • BridgeDbR: R package that exposes BridgeDb functionality
  • Metabolite identifier mapping database (HMDB + ChEBI)
  • Interaction identifier mapping database (EBI-Rhea)

Pathway and Network Analysis

  • GoElite: extended pathway and Gene Ontology analysis
  • Apps for Cytoscape:
    • CyTargetLinker: a generic Cytoscape app to build regulatory networks
    • SemScape: Visualizes Semantic Data Landscapes (Google Summer of Code project 2012)

Semantic Web

  • Open PHACTS: Platform to reduce barriers in drug discovery
  • WikiPathways RDF: SPARQL endpoint of WikiPathways to query pathway data
  • rrdf: a R package to handle RDF data
  • ops4j: java Client library for Open PHACTS servers
  • ropenphacts: a R package to interact with Open PHACTS servers

Small Molecules