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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 Group-wise ANOVA Simultaneous Components Analysis (G-ASCA). Get the code.  (avalaible in the MEDA toolbox)

Reference: Saccenti, E.; Camacho J.; Smilde, A.; Group-wise principal component analysis for exploratory data analysis. Metabolomics 2018. 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.

Matlab code for Covariance Simultaneous Component Analysis (COVSCA). 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.

 


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.