Girke Lab Research and Teaching Site


R/Bioconductor Packages

  • systemPipeR: NGS workflow and report generation environment
  • ChemmineR: Cheminformatics Toolkit for R 
  • ChemmineOB: R interface to a subset of OpenBabel functionalities 
  • fmcsR: Flexible Maximum Common Substructure (FMCS) Searching (also see MCS
  • eiR: Accelerated similarity searching of small molecules 
  • bioassayR: R library for Bioactivity analysis


  • AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
  • BRANCHboosting RNA-Seq assemblies with partial or related genomic sequences
  • SEED: Clustering next generation sequences
  • MCS: A maximum common substructure-based algorithm for searching and predicting drug-like compounds
  • EI Search: ultra-fast compound similarity searching

Web Applications

  • ChemMine Tools: online tool box for small molecule analysis
  • Sub-HMM: identification of conserved protein regions
  • EI Search: ultra-fast compound similarity searching