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A flexible R package for nonnegative matrix factorization

By Renaud Gaujoux and Cathal Seoighe
Topics: Software
Publisher: BioMed Central
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Provided by: PubMed Central

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  5. (2008). Gallopoulos E: SVD based initialization: A head start for nonnegative matrix factorization. Pattern Recognition
  6. (2001). Hou X: Learning Spatially Localized, Parts-Based Representation. Convergence
  7. (2005). Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics
  8. (2006). Initializations for the nonnegative matrix factorization
  9. (1999). Learning the parts of objects by non-negative matrix factorization. Nature
  10. (2007). Mesirov JP: Metagene projection for cross-platform, cross-species characterization of global transcriptional states
  11. (2004). Mesirov JP: Metagenes and molecular pattern discovery using matrix factorization.
  12. (2008). Non-negative matrix factorization for the analysis of complex gene expression data: identification of clinically relevant tumor subtypes. Cancer informatics
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  14. (2004). Non-negative matrix factorization with sparseness constraints.
  15. (2008). Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS computational biology
  16. (2006). Ochs MF: LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates. BMC bioinformatics
  17. (2006). Pascual-marqui RD: Nonsmooth nonnegative matrix factorization (nsNMF).
  18. (2006). Pascual-Montano A: Biclustering of gene expression data by non-smooth non-negative matrix factorization.
  19. (2008). Pattern expression nonnegative matrix factorization: algorithm and applications to blind source separation. Computational intelligence and neuroscience
  20. (2008). Position-Dependent Motif Characterization Using Nonnegative Matrix Factorization. Bioinformatics
  21. (1994). Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values. Environmetrics
  22. (2008). Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous nonNegative. Pacific Symposium on Biocomputing
  23. (2009). REvolution Computing: doMC: Foreach parallel adaptor for the multicore package
  24. (2001). Seung H: Algorithms for non-negative matrix factorization. Advances in neural information processing systems
  25. (2006). Si: New Algorithms for Non-Negative Matrix Factorization in Applications to Blind Source Separation. Acoustics, Speech and Signal Processing,
  26. (2007). Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics (Oxford,
  27. (2010). Sun Grid Engine []. doi: 10.1186/1471-2105-11-367 Cite this article as: Gaujoux and Seoighe, A flexible R package for nonnegative matrix factorization BMC Bioinformatics
  28. (2005). Theme discovery from gene lists for identification and viewing of multiple functional groups.
  29. (2003). Tidor B: Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res
  30. (2007). Wang G: Parallel implementation of nonnegative matrix factorization algorithms using high-performance computing cluster
  31. (2009). XJJ: Automated multidimensional phenotypic profiling using large public microarray repositories.
  32. Zdunek R: NMFLAB MATLAB toolbox for non-negative matrix factorization [].

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