Software

Logistic PCA toolbox
Software to accompany Logistic principal component analysis via non-convex singular value thresholding
HetroFusion toolbox
Software to accompany Heterofusion: Fusing genomics data of different measurement scales
GSCA of binary and quantitative data
Software to accompany Generalized Simultaneous Component Analysis of Binary and Quantitative data
PCA of binary genomics data
Scripts to reproduce the data in Principal component analysis of binary genomics data
PetriNetSimulation
Petrinet Simulator
SATFO
Simulated Annealing Toolbox For Optimization
MetStat
A diverse collection of metabolomics related statistical tools
Invalidation by SPCA
Simplivariate method
The program provides an implementation of recently introduced simplivariate models. The program expresses relations between functional genomics data in easily interpretable simplivariate components.
Reference: Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data
HC4N Toolbox
This R-toolbox contains the HC4N algorithm and supplementary functions explained in the publication Towards a Hierarchical Strategy to Explore Multi-Scale IP/MS Data for Protein Complexes .

dynEMR
Dynamic elementary mode regression discriminant analysis for non-steady state flux data.
COVSCA
Vertex-edge incidence matrix by using the zero slopes method.
Fourth order approximation of the time derivatives of metabolite concentrations and calculation of the Jacobian.
Time lagged correlation matrix
Reference: Reverse engineering of metabolic networks, a critical assessment
Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot
Mol. BioSyst, Advance Article (2011)
Grey component analysis
Endocrine pulse identification
Reference: Endocrine pulse identification using penalized methods and a minimum set of assumptions
Daniel J. Vis, Johan A. Westerhuis, Huub C. J. Hoefsloot, Hanno Pijl, Ferdinand Roelfsema, Jan van der Greef, and Age K. Smilde
Am J Physiol Endocrinol Metab Vol. 298 (2009), pages 146-155, 2010
Crossfit: Model generating Global, Local and Crossfit models of crossed data with two factors, time and treatment.
MLPLSDA: Multilevel Data Analysis
Tutorial Multilevel Data Analysis
RV_modified: Modified RV-coefficient for matrix correlations for high dimensional data
Reference: Matrix correlations for high-dimensional data: the modified RV-coefficient
A.K. Smilde, H.A.L. Kiers, S. Bijlsma, C.M. Rubingh and M.J. van Erk
Bioinformatics Advance Access published December 10 2008 (Oxford University Press)
DQ2: Calculates the discriminant Q² value
Reference: Discriminant Q² (DQ²) for improved discrimination in PLSDA models
Johan A. Westerhuis, Ewoud J. J. van Velzen, Huub C. J. Hoefsloot and Age K. Smilde
Metabolomics: Springer link date 30 August 2008
PCDA: Principal Component Discriminant Analysis
MALS: Maximum Likelihood Scaling (MALS)
ASCA: ANOVA Simultaneous Component Analysis
CPDScv: Crossvalidation for CPDS
DOSC: Direct Orthogonal Signal Correction
MMC_CRM: Multiway Multiblock Component and Covariates Regression Models
Bagged Clustering k-means: Bagged Clustering k-means
MSCA: Multilevel Simultaneous Component Analysis
PCAW: Weighted Principal Component Analysis
PCOVR: Principal Covariates Regression/PARAFAC
SmoothPCA: Smooth PCA

Software

Matlab© M-files

Matlab^© M-files