Software
The software on this web page is provided "as is" with no warranty whatsoever. Please acknowledge contributions based on this software in your publications.
Code written in R
- mvdalab: Multivariate Data Analysis Laboratory
An open-source project implementation of latent variable methods and multivariate modeling tools. It contains amongst others PCA, Biplots, NIPALS PCA, PLS, several VIP methods, missing value handling, Procrustes analysis, Multivariate EWMA and data simulation functions. - Scripts (zip, 1,1 MB) accompanying the paper "Robust ANOVA for microarray data (zip, 1,1 MB), by J.R.de Haan et al., Chemom. Intell.Lab. Syst.(2009). For details, contact Jorn de Haan.
- Scripts accompanying the paper "Interpretation of ANOVA models for microarray data using PCA", by J.R. de Haan et al., Bioinformatics (2006): anpca.synth.R (zip, 2,1 kB) and biplot.R (zip, 915 bytes). For details, contact Jorn de Haan.
- ptw, a package for parametric time warping of chromatographic data. Authors: Jan Gerretzen, Paul Eilers, Hans Wouters, Tom Bloemberg and Ron Wehrens
- GoTime (zip, 537 kB), for visualization of GO enrichment in time for microarray data sets.
Author: Jorn de Haan - pls, routines for multivariate regression by PLS and PCR. Supersedes package pls.pcr.
Authors: Ron Wehrens and Bjorn-Helge Mevik - kohonen, supervised and unsupervised self-organising maps.
Author: Ron Wehrens - wccsom, self-organising maps for patterns containing shifting peaks, such as X-ray powder patterns.
Author: Ron Wehrens - CompClus (zip, 19 kB), comparison of clusterings/partitionings.
Author: Ron Wehrens - GenAlg, an R package for genetic algorithm optimisation, a.o. variable selection and parameter optimisation.
Author: Egon Willighagen. - 'Supplementary material of "Model-based clustering for image segmentations and large datasets via sampling" by Wehrens, Buydens, Fraley and Raftery, Techn. Report no. 424, Dept. of Statistics, University of Washington, February 2003, and Journal of Classification 21:231-253 (2004), DOI: 10.1007/s00357-004-0018-8 : Data : St. Paulia data (zip, 242 kB) (courtesy of J. Noordam, Agrotechnology and Food Innovations B.V., Wageningen, NL) A three-column gzipped ascii file: the image size is 304 times 268.; R/Splus scripts Import data (zip, 259 bytes), Strategy I (zip, 416 bytes), Strategy II (zip, 431 bytes) , Strategy III (zip, 773 bytes) , Strategy IV (zip, 427 bytes)
Code written in Matlab
- OTflow code & tutorial: algorithm for optimal transformation of Multicolor Flow Cytometry data and user manual by Rita Folcarelli, Gerjen Tinnevelt 2021
- ENDBOSS source code and demonstration 2020 by Tim Offermans
- Data G.Tinnevelt-Faraday Discussions 2019 as used in "Resolving complex hierarchies in chemical mixtures: how chemometrics may serve in understanding the immune system"; Tinnevelt, Gerjen Herman, and Jeroen Jasper Jansen. Faraday discussions218 (2019): 317-338.
- ECLIPSE
- sMC varialbe importance, accompanying the papers "Interpretation of variable importance in Partial Least Squares with Significance Multivariate Correlation (sMC)" by T.N. Tran et al. & "Variable Importance in PLS in the Presence of Autocorrelated Data - Case studies in Industrial Manufacturing Processes" by N.L. Afanador et al. For details contact T.N. Tran or N.L. Afanador.
- WRTPLS for number of components in PLS, accompanying the paper "Weight Randomization Test for the selection of the number of components in PLS models" by T.N. Tran et al. For details contact T.N. Tran.
- DAMACY-and-Fusion (zip, 911 kB)
- POCHEMON (zip, 352 kB)
- BDK-SOMPLS.zip (zip, 5,1 MB), a toolbox for using XYF, BDK, SOMPLS and KPLS algorithms.
Author: Willem Melssen - KNNCLUST (zip, 2,2 kB), a toolbox for density-based clustering (see publication 03/02).
Author: Thanh Ngoc Tran - MULVADO (zip, 29 kB), a toolbox for the multivariate analysis of DOSY NMR data. Version 1.3, Jan 27, 2006.
An example of an experimental dataset in Matlab format (6.3 Mb) can be found here (zip, 5,2 MB) (courtesy of J. Pikkemaat, Philips Research Eindhoven).
Author: Ruifen Huo