# 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.

## ccdf

An R package to perform single-cell RNA-seq differential expression analysis and more generally complex hypothesis testing. 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 Ferte. 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.