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Semantic related software

Code for RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource.  Get the code.  Try it in the Galaxy environment!  Start here

Reference:  van Dam, J. C. J.; Koehorst, J. J.; Schaap, P. J.; Martins dos Santos V. A. P.;  Suarez-Diez, M., RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource Journal of Biomedical Semantics 2015, 6(39), Get the paper.

Code for SAPP – Semantic Annotation Platform with Provenance. Get the code; Get the executables; Get the documentation.

Reference:  Koehorst J. J.; Dam J. C.;  Saccenti E., Martins Dos Santos, V. A. P. ; Suarez-Diez, M.; Schaap,  P. J., SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles Bioinformatics 2017, Get the paper.

Code for EMPUSA a code generator for the development of ontologies, Get the code.

Reference: van Dam, J. C. J.; Koehorst, J. J.; Vik, J. O.; Schaap, P. J.;   Suarez-Diez, M. Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining bioRxiv, 2017. Get the paper


Matrix analysis and statistical software

Matlab code for COVSCA COVariance Simultaneous Component Analysis. Get the code.

Reference: Smilde, A. K.; Timmerman, M. E.; Saccenti E.; Jansen, J. J.; Hoefsloot H. C. J., Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances Journal of Chemometrics 2015, 29, 277-278. Get the paper.

Winning paper of the Kowalski Prize 2017  for the Best application paper in chemometrics/statistics! Read here.

 

Matlab code for Horn’s parallel analysis. Get the code.
Matlab code for Tracy-Widom testing. Get the code.

Reference: Saccenti, E.; Timmerman, M. E., Reconsidering Horn’s parallel analysis from a Random Matrix Theory point of view  Psychometrika 2016, 82(1), 186-209.  Get the paper


Matlab code to generate the normalization moment for the Tracy-Widom distribution for autoscaled real matrices (correlation case). Get the code.

Reference: Saccenti, E.; Smilde, A. K.; Westerhuis, J. A.; Hendriks, M. M. W. B., Tracy–Widom statistic for the largest eigenvalue of autoscaled real matrices Journal of Chemometrics 2011, 25, 644-652. Get the paper.


Matlab codes for sample size determination in PCA. Get the code.

Reference: Saccenti, E.; Timmerman, M. E., Approaches to Sample Size Determination for Multivariate Data: Applications to PCA and PLS-DA of Omics Data Journal of Proteome Research 2016, 15, 2379-2393. Get the paper.

Matlab code for Group-wise principal component analysis (GPCA). Get the code.  (avalaible in the MEDA toolbox)

Reference: Camacho, J.; Rodriguez-Gomez, R.; Saccenti, E. Group-wise principal component analysis for exploratory data analysis. Journal of Computational and Graphical Statistics 2017, 27. Get the paper.

Matlab code for Group-wise partial least square regression (GPLS). Get the code.  (avalaible in the MEDA toolbox)

Reference: Camacho, J.; Saccenti, E. Group-wise partial least square regression. Journal of Chemometrics, 2017. Get the paper.


Network analysis software

R code for the PCLRC algorithm. Get the code.

Reference: Saccenti, E.; Suarez-Diez, M.; Luchinat, C.; Santucci, C.; Tenori, L., Probabilistic Networks of Blood Metabolites in Healthy Subjects As Indicators of Latent Cardiovascular Risk Journal of Proteome Research 2014, 14, 1101-1111. Get the paper.

R code for the DECA algorithm. Get the code.

Reference:  Venkatasubramanian, P. B.; Toydemir, G.;  de Wit, N.; Saccenti, E.; Martins dos Santos, V. A. P.;  van Baarlen, P.; Wells, Jelly.;  Mes, J.;  Use of microarray datasets to generate Caco-2-dedicated networks and to identify reporter genes of specific pathway activity Scientific Reports 2017, 7:6778.  Get the paper.