High-Dimensional Biostatistics for Drug Safety and Genomics, CESP, INSERM
Here you will find a selection of resources made available by members of the High-Dimensional Biostatistics for Pharmacoepidemiology and Genomics Team (INSERM, Paris Saclay University)
R packages hosted on the CRAN
- gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models : https://cran.r-project.org/package=gaston
- Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
- milorGWAS: Mixed Logistic Regression for Genome-Wide Analysis Studies (GWAS) : https://cran.r-project.org/package=milorGWAS
- Ravages: Rare Variant Analysis and Genetic Simulations : https://cran.r-project.org/package=Ravages
- Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.
- salad: Simple Automatic Differentiation : https://cran.r-project.org/package=salad
- adapt4pv: Adaptive Approaches for Signal Detection in Pharmacovigilance : https://cran.r-project.org/package=adapt4pv
- houba: Manipulation of (Large) Memory-Mapped Objects (Vectors, Matrices and Arrays) : https://cran.r-project.org/package=houba
- Manipulate data through memory-mapped files, as vectors, matrices or arrays. Basic arithmetic functions are implemented, but currently no matrix arithmetic. Can write and read descriptor files for compatibility with the ‘bigmemory’ package.
Supplementary Material of Publications
- Quentin E, Ahmed I, Duong CH, Tubert-Bitter P, Escolano S. Covid-19 Vaccination During Pregnancy in France: a Descriptive Study of Uptake Using the National Healthcare data System. Vaccine. 2025;58:127223. https://doi.org/10.1016/j.vaccine.2025.127223
- SAS macros for database constitution (identification of pregnancies, determination of pregnancy outcomes, mother-child linkage) : https://github.com/sylvieescolano/SNDS_pregnancy
- Duong C-H, Quentin E, Demailly R, Quantin C, Escolano S, Botton J, Tubert-Bitter* P, & Ahmed* I (2026). Association between exposure to non-steroidal anti-inflammatory drugs in pregnancy and miscarriage risk : A French nationwide retrospective cohort study. BMJ Open, 16(3), e111456. https://doi.org/10.1136/bmjopen-2025-111456
- R codes for statistical analyses : https://github.com/HiDiBiostat/Association-between-exposure-to-NSAIDs-in-pregnancy-and-miscarriage
