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Definition
of MATLAB M-files/tools for microarray analysis
Suggested readings
MATLAB
Mfiles for microarray analysis (in alphabetical order)
[ Dimension reduction
methods for tumor classification | Fuzzy
C-Means for Clustering | F-scan
| Greedy mixture learning
for multiple motif discovery | MA-ANOVA
| MatArray toolbox | MGraph | P-scan | PCA disjoint models for multiclass cancer
analysis | Quantum Clustering ]
| M-file/tools | Author | Features | Version | Date | Licence | Remarks |
| Dimension reduction methods for tumor classification | Antoniadis A, Lambert-Lacroix S, Leblanc F. Laboratoire IMAG-LMC, University Joseph Fourier, | Dimension reduction statistical
techniques in conjunction with nonparametric discriminant procedures
for
classification |
- |
- |
Free |
Reference [PubMed] |
| Fuzzy C-Means for
Clustering |
Doulaye Dembélé
and Philippe Kastner IGBMC CNRS-INSERM-ULP, |
Fuzzy C-Means for Clustering
Microarray Data |
- |
- |
Free? |
Download; Reference [PubMed] |
| F-scan | P. J. Munson, V. V. Prabhu, L. Young; Analytical Biostatistics Section; Mathematical and Statistical Computing Laboratory; Center for Information Technology; National Institutes of Health | Quantification and analysis of fluorescently probed microarrays; scatterplots; multiple image comparison; data merging and web links. | 1.3 | 2001/07/30 | Free for academic | Download available upon registration; Manual; sample images for testing [pc][mac][unix]; reference [PubMed] |
| Greedy mixture learning for multiple motif discovery | Blekas K, Fotiadis DI, Likas A. Department of Computer Science, University of Ioannina | Discovering probabilistic motifs
in a set of biological sequences by learning a mixture of motifs model
through likelihood maximization. |
- |
- |
Free |
Download;
Reference [PubMed] |
| MA-ANOVA | Gary Churchill's Statistical Genetics Group, The Jackson Laboratory | MA-ANOVA is a set of functions written in Matlab for the analysis of variance on microarray data. | 1.2 | 2002/03/20 | free for academic | registration before download; available in both windows and linux format; sample data 1; sample data 2; Readme;release notes; reference 1[pdf]; reference 2[pdf]; |
| MatArray toolbox | David Venet, | Its main features are: Advanced normalization schemes; Very efficient implementation of hierarchical clustering, with leaf ordering and export to TreeView; Efficient implementation of K-means clustering. | ? | ? | Free | start-up
guide; reference;Toolbox
(binaries non compiled); Toolbox
(compiled for win32); Help
files; Reference [PubMed] |
| MGraph |
Wang J, Myklebost O, Hovig E. Department of Tumour Biology, Norwegian Radium Hospital, Norway |
applies graphical models as a natural environment to formulate and solve problems in microarray data analysis; allows the user to predict genetic regulatory networks by a graphical gaussian model (GGM), and to quantify the effects of different experimental treatment conditions on gene expression profiles by a graphical log-linear model (GLM). | ? |
? |
Free |
Reference [PubMed] |
| P-scan (Peak quantification using Statistical Comparative ANalysis) | P. J. Munson, V. V. Prabhu, L. Young; Analytical Biostatistics Section; Mathematical and Statistical Computing Laboratory; Center for Information Technology; National Institutes of Health | Quantification and analysis membrane cDNA array; scatterplots; multiple image comparison; data merging and web links. | 1.2 | 2001/06/26 | Free for academic | registration before download; manual; samples images available; reference [PubMed] |
| PCA disjoint models for
multiclass cancer analysis |
Bicciato S, Luchini A, Di Bello C. Department of Chemical Process Engineering, University of Padova | A computational procedure for marker identification and for classification of multiclass gene expression data through the application of disjoint principal component models | - |
- |
? |
source codes are available from
the authors. Reference [PubMed] |
| Quantum Clustering |
David Horn, Assaf Gottlieb and Inon Axel | Performing and evaluating the
Quantum Clustering method for data in arbitrary number of dimensions |
? |
? |
Free? |
Reference 1 [PubMed][ps];
Reference 2 [PubMed][ps]; Reference 3 [ps]; |