epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

A package for detecting epistasis by machine learning

Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)

Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e.g., protein functions).

NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model

The multivariate MArginal ePIstasis Test

Code and simulations using interaction-LD score regression

Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"

A tool to predict missing data in sparsely sampled genotype-phenotype maps

Parallel Implementations of the Empirical Bayesian Elastic Net Cross-Validation in R

Case-control genetics datasets evolved to be epistatic

A fast and scalable method to detect epistasis in complex traits from biobank-scale studies

PAGER is an efficient genotype encoding strategy designed to improve the detection of non-additive genetic variation in complex trait association studies. PAGER dynamically encodes genetic variants by normalizing mean phenotypic differences between genotype classes.

The W-Model, a tunable Black-Box Discrete Optimization Benchmarking (BB-DOB) problem, implemented for the BB-DOB@GECCO Workshop.

Learning the language of phylogeny with MSA Transformer

Inference of Epistatic Gene Networks

A library for calculating penetrance tables of any bivariate epistasis model.

GWAS third-level epistatic search tool for cluster architectures

A Python tool to calculate penetrance tables for high-order epistasis models

Experimental-design methods for budgeted protein-epistasis mapping with zero-shot ESM-2 signals; evaluated on GB1.