Dendsort: Modular leaf ordering methods for dendrogram representations in R

F1000Research

Volumn 3, Issue , 2014, Pages

  Sakai, Ryo ^a   Winand, Raf ^a   Verbeiren, Toni ^a   Moere, Andrew Vande ^a   Aerts, Jan ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; CLUSTER HEAT MAP; DATA ANALYSIS; DATA PROCESSING; DENDSORT; HEURISTIC; INTERMETHOD COMPARISON; LINEAR OORDER; LINEAR SYSTEM; PHYLOGENETIC TREE; RANDOM ORDER; RANDOMIZATION; STATISTICAL CONCEPTS;

EID: 84915818649     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.4784.1     Document Type: Article

References (21)

1. Wilkinson L Friendly M: The History of the Cluster Heat Map. Am Stat. 2009;63(2):179-184. 10.1198/tas.2009.0033
2. Gehlenborg N O'Donoghue SI Baliga NS: Visualization of omics data for systems biology. Nat Methods. 2010;7(3 Suppl):S56-68. 20195258 10.1038/nmeth.1436
3. de Souto MC Costa IG de Araujo DS: Clustering cancer gene expression data: a comparative study. BMC Bioinformatics. 2008;9:497. 19038021 10.1186/1471-2105-9-497 2632677
4. Hastie T Tibshirani R Friedman J: The Elements of Statistical Learning. Springer Series Statistics. 2009. 10.1007/978-0-387-84858-7
5. Tan P Kumar V Steinbach M: Introduction to data mining. Boston: Pearson Addison Wesley, 1st ed edition.2005. Reference Source
6. Bar-Joseph Z Gifford DK Jaakkola TS: Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001;17(Suppl 1):S22-9. 11472989 10.1093/bioinformatics/17.suppl_1.S22
7. Gehlenborg N Wong B: Points of view: Heat maps. Nat Methods. 2012;9(3):213. 10.1038/nmeth.1902
8. Morris SA Asnake B Yen GG: Dendrogram seriation using simulated annealing. Information Visualization. 2003;2(2):95-104. 10.1057/palgrave.ivs.9500042
9. James G Witten D Hastie T: An Introduction to Statistical Learning, of Springer Texts in Statistics. Springer New York, New York, NY.2013; 103. 10.1007/978-1-4614-7138-7
10. Gruvaeus G Wainer H: Two Additions to Hierarchical Cluster Analysis. J Math Stat Psychol. 1972;25(2):200-206. 10.1111/j.2044-8317.1972.tb00491.x
11. Chae M Chen JJ: Reordering hierarchical tree based on bilateral symmetric distance. PLoS One. 2011;6(8):e22546. 21829631 10.1371/journal.pone.0022546 3150382
12. Hahsler M Hornik K Buchta C: Getting Things in Order: An Introduction to the R Package seriation.2001. Reference Source
13. Eisen MB Spellman PT Brown PO: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95(25):14863-14868. 9843981 10.1073/pnas.95.25.14863 24541
14. Quackenbush J: Computational analysis of microarray data. Nat Rev Genet. 2001;2(6):418-27. 11389458 10.1038/35076576
15. Buchta C Hornik K Hahsler M: Getting things in order: an introduction to the R package seriation. J Stat Softw. 2008;25(3). Reference Source
16. R Core Team and contributors worldwide. R: Edgar Anderson's Iris Data.
17. Ware C: Information Visualization: Perception for Design. Morgan Kaufmann Publishers Inc., San Francisco.2004. Reference Source
18. Ware C: Color sequences for univariate maps: theory, experiments and principles. IEEE Comput Graph Appl. 1988;8(5):41-49. 10.1109/38.7760
19. The Cancer Genome Atlas Research Network. Comprehensive Molecular Characterization of Gastric Adenocarcinoma. Nature. 2014. 10.1038/nature13480
20. Tufte ER: The Visual Display of Quantitative Information. Graphics Press, Cheshire, CT, USA.1986. Reference Source
21. Sakai R Winand R Verbeiren T: R package dendsort for modular leaf ordering methods. Zenodo. 2014. Data Source