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.
citcdf
An R package to perform conditional independence testing using empirical conditional cumulative distribution function estimations for single-cell RNA-seq differential expression analysis. Available on GitHub.
CytOpT
An R package to perform Optimal transport for gating transfer in cytometry data with domain adaptation. Available on CRAN, 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.
dearseq 
An R package to perform Differential Expression Analysis for RNA-seq data through a robust variance component test. Available on Bioconductor, 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 developed with 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 developed with Viviane Philips, Mélanie Prague & Cécile Proust-Lima. 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 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, developed with Thomas Ferté. Available on CRAN, development version on gitlab.
sGBJ
An R package to perform Gene Set Analysis for time-to-event outcomes using a Survival Extension of the Generalized Berk-Jones Test. Available on CRAN, development version available on GitHub.
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.
All illustrations (except CytOpt) by Jérôme Dubois.