Rare Variant Analysis and Genetic Simulations
SNVs and Indels annotation with adjusted CADD scores
Indels annotation with adjusted CADD scores
SNVs annotation with adjusted CADD scores
Bed matrix for variants associated to multiple genomic regions
Linear regression on a genetic score
Linear regression on a multiple genetic scores within a genomic region
Logistic or multinomial regression on a genetic score
Logistic or multinomial regression on a multiple genetic scores within...
Linear, logistic or multinomial regression on a genetic score
Linear, logistic or multinomial regression on a multiple genetic score...
Score matrix for burden tests
Cohort Allelic Sum Test
Rare variants filtering
Variant filtering based on frequency and median adjusted CADD by CADD ...
Genes positions
Genotypic frequencies calculation for data simulations
GRR matrix for genetic data simulation
Jaccard index
Single variant association test with categorical phenotype
Null Model for SKAT and burden tests
RAVA-FIRST: RAre Variant Association using Functionally-InfoRmed STeps
Power of RVAT based on simulations and theoretical calculations (CAST)...
Simulation of genetic data using GRR values
Simulation of genetic data based on haplotypic frequencies
Power of RVAT based on simulations with haplotypes
Simulation of genetic data based on haplotypes and a libaility model
Variants annotation based on 'CADD regions' and genomic categories
Variants annotation based on gene positions
Variants annotation based on regions and subregions positions
Multi group SKAT test using bootstrap sampling
Multi group SKAT test using Liu et al. approximation
Multi group SKAT test using bootstrap sampling
SKAT test
Multi group SKAT test using Liu et al. approximation
Exemple of functional categories
WSS genetic score
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.