complex-traits

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.

PhenoPLIER

A list of cool software for genetic analysis and the like

A light and flexible R package to evaluate GWAS-based gene prioritization methods for complex traits.

Papers relating to neuropsychiatric disorders

A heritability-optimized scoring method using multivariate adaptive regression splines that incorporates 75 variant- and gene-level features. RovHer leverages exome-wide association statistics to train models estimating the probability of RV functional impact.

PhenoPLIER manuscript

Genetics Dissection of Complex Traits

Benchmarking 86 heritability estimation configurations and downstream polygenic risk score performance across UK Biobank phenotypes. Associated paper: arXiv:2604.02394

Pipeline to investigate multimorbidity of complex traits/phenotypes by integrating chromatin interaction and expression quantitative trait loci data.

A Systematic Analysis of Gene-Gene Interaction Networks Underlying Human Polygenic Phenotypes