Algorithms and framework for Nonnegative Matrix Factorization (NMF)

How to cite

Gaujoux R and Seoighe C (2010). “A flexible R package for nonnegative matrix factorization.” BMC Bioinformatics, 11(1), pp. 367. ISSN 1471-2105,,

This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

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  • R version: R >= 3.1.0
  • Depends: methods, utils, pkgmaker, registry, rngtools, cluster
  • Imports: graphics, stats, stringr, digest, grid, grDevices, gridBase, colorspace, RColorBrewer, foreach, doParallel, ggplot2, reshape2, dendextend
  • Suggests: RcppOctave, fastICA, doMPI, bigmemory, synchronicity, corpcor, xtable, devtools, knitr, bibtex, RUnit, mail, Biobase


  • Renaud Gaujoux
  • Cathal Seoighe


  • Renaud Gaujoux (renaud at