Software

VICI


A Shiny app to perform for accurate estimation of vaccine induced cellular immunogenicity with bivariate linear modeling. Available at https://shiny-vici.apps.math.cnrs.fr/, or locally through the vici R package.




dearseq


An R package to perform Differential Expression Analysis for RNA-seq data through a robust variance component test. Development version available on GitHub.





cytometree


An R package to perform Automatic gating and annotation of cytometry data. Available on CRAN, development version available on GitHub.





kernscr


An R package to perform KERNel machine score test for pathway analysis in the presence of Semi-Competing Risks. Available on CRAN, development version available on GitHub.





foodingraph


An R package to perform Food Network Inference and Visualization developped by Victor Gasque. Available on CRAN, development version on GitHub.





ludic


An R package to perform probabilistic record Linkage Using only DIagnosis Codes without direct identifiers, using C++ code to speed up computations. Available on CRAN, development version on GitHub.





marqLevAlg


An R package to perform (parallelized) optimization of convex multiparametric functions. Available on CRAN, development version on GitHub.





NPflow


An R package to perform Dirichlet process mixture of multivariate normal, skew-normal or skew $t$-distributions modeling oriented towards flow-cytometry data preprocessing applications, using C++ code to speed up computations. Available on CRAN, development version on GitHub.





PheVis an automatic instant phenotyping from EHR data at the visit resolution


An R package to perform automatic instant phenotype prediction at the visit level from EHR data that can be used for either chronic or acute conditions. Development version available on gitlab.





TcGSA


An R package to analyze longitudinal gene-expression data at the gene set level. Available on CRAN, development version on GitHub.





tcgsaseq


An R package to perform gene set analysis of longitudinal RNA-seq data with variance component score test, accounting for data heteroscedasticity through precision weights. Available on CRAN, development version on GitHub.





vici


An R package to perform accurate estimation of vaccine induced cellular immunogenicity with bivariate linear modeling. Available on CRAN, development version on GitHub.