PermutMatrix

PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. PermutMatrix is a program to perform graphical analysis of a dataset. It implements several types of cluster analysis and a variety of methods for statistical seriation. Numerical values from the dataset are converted into a gradation of colours. Then rows and/or columns are permuted in such a way that a structure appears. A row or column ordering that reveals a statistical organisation in the dataset is searched. This approach has been widely used for many years in archaeology, sociology and operational research. It has new applications in biology, owing to Eisen’s work on the use of hierarchical clustering for gene expression data


References in zbMATH (referenced in 12 articles )

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  1. Concas, Anna; Fenu, Caterina; Rodriguez, Giuseppe: \textttPQser: a Matlab package for spectral seriation (2019)
  2. Anna Concas, Caterina Fenu, Giuseppe Rodriguez: PQSER: A Matlab package for spectral seriation (2017) arXiv
  3. Hahsler, Michael: An experimental comparison of seriation methods for one-mode two-way data (2017)
  4. Vigneron, V.; Chen, H.: A multi-scale seriation algorithm for clustering sparse imbalanced data: application to spike sorting (2016)
  5. Préa, Pascal; Fortin, Dominique: An optimal algorithm to recognize Robinsonian dissimilarities (2014)
  6. Palubeckis, Gintaras: An improved exact algorithm for least-squares unidimensional scaling (2013)
  7. Wittek, Peter: Two-way incremental seriation in the temporal domain with three-dimensional visualization: making sense of evolving high-dimensional datasets (2013)
  8. Chepoi, Victor; Seston, Morgan: Seriation in the presence of errors: a factor 16 approximation algorithm for (l_\infty)-fitting Robinson structures to distances (2011)
  9. Newman, Aaron M.; Cooper, James B.: Autosome: a clustering method for identifying gene expression modules without prior knowledge of cluster number (2010) ioport
  10. Chepoi, Victor; Fichet, Bernard; Seston, Morgan: Seriation in the presence of errors: NP-hardness of (l_\infty)-fitting Robinson structures to dissimilarity matrices (2009)
  11. Chepoi, Victor; Seston, Morgan: An approximation algorithm for (\ell_\infty) fitting Robinson structures to distances (2009)
  12. Michael Hahsler; Kurt Hornik; Christian Buchta: Getting Things in Order: An Introduction to the R Package seriation (2008) not zbMATH