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Software - Open Source:
ClutrFree

Synopsis:

ClutrFree is a cluster viewer package available as a Java application. ClutrFree provides essentially the ability to compare microarray clusters issued from different experiments, i.e. the same algorithm used with different parameters or different algorithms. ClutrFree features a procedure to construct a tree from those clusters to infer which ones are more stable among different experiments. Also, ClutrFree displays genes and their memberships along with annotations and ontology. Source code, pre-compiled bytecode, documentation and test datasets are provided. The source code is released under the GNU general public license (GPL).

Downloads:


  • ClutrFree Demonstration Data
  • Using ClutrFree with TIGR MeV
    • Sample MEV analysis for the Cho Yeast Cell Cycle Data Set: (Data set reference: Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg
      TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A genome-wide transcriptional
      analysis of the mitotic cell cycle. Mol Cell 1998; 2:65-73.),
      and then a link to MeV
    • MeV: MultiExperiment Viewer is available from the following link
       
  • Functional Genomics Pipeline (FGDP) to ClutrFree Format Conversion

  • Documentation:

    Related Software:

    • Bayesian Decomposition - A pattern recognition algorithm which uses Bayesian statistics and Markov chain Monte Carlo sampling to determine the physically significant basis vectors for a data set.

    Reference:

    • Bidaut G. & Ochs M.F. (2004) ClutrFree: cluster tree visualization and interpretation. Bioinformatics Nov 1;20(16):2869-71.

    Contact Information:

    Ghislain Bidaut
    Biostatistics and Bioinformatics Facilities
    Fox Chase Cancer Center
    Philadelphia, PA 19111