GitHub topics: epistasis

Repositories

harmslab/epistasis

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

Language: Python - Size: 4.62 MB - Last synced at: 8 days ago - Pushed at: about 2 years ago - Stars: 35 - Forks: 11

lcrawlab/sme

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

Language: C++ - Size: 3.3 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

gpaasi/epistasis-malaria-rbc-polymorphisms

A systematic review of epistatic interactions among co-inherited malaria-protective red blood cell polymorphisms, synthesizing evidence on additive, synergistic, and antagonistic effects across infection, density, clinical malaria, and mortality outcomes.

Language: R - Size: 5.91 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

lcrawlab/mvMAPIT

The multivariate MArginal ePIstasis Test

Language: R - Size: 37.8 MB - Last synced at: about 7 hours ago - Pushed at: 11 months ago - Stars: 13 - Forks: 1

mspancho/graphistasis

Using deep learning frameworks (Multilayer Perceptron and Graph Neural Network) to mine gene-gene (epistatic) interactions for neurologic disease in the BioSNAP DG-AssocMiner dataset.

Language: Jupyter Notebook - Size: 36.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Cassie818/MsaPhylo

Learning the language of phylogeny with MSA Transformer

Language: Python - Size: 40.3 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 2 - Forks: 0

EpistasisLab/PAGER

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.

Language: Python - Size: 531 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 3 - Forks: 1

lcrawlab/i-LDSC

Code and simulations using interaction-LD score regression

Language: Python - Size: 15.4 GB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 1

harmslab/gpseer

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

Language: Python - Size: 1.57 MB - Last synced at: 15 days ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 3

thomasWeise/BBDOB_W_Model

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

Language: Java - Size: 155 KB - Last synced at: 4 months ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 3

complexgenome/CUMC_taub

Language: R - Size: 374 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

greenelab/model-free-data

Case-control genetics datasets evolved to be epistatic

Language: PostScript - Size: 13.9 MB - Last synced at: 4 months ago - Pushed at: about 7 years ago - Stars: 5 - Forks: 2

pecanka/epidetector

EpiDetector: A tool for identifying epistasis

Language: Fortran - Size: 36 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

bglezseoane/pytoxo

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

Language: Python - Size: 14 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Chester75321/GenEpi

A package for detecting epistasis by machine learning

Language: Python - Size: 11.8 MB - Last synced at: 15 days ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 9

UDC-GAC/mpi3snp

GWAS third-level epistatic search tool for cluster architectures

Language: C++ - Size: 552 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

amirmohan/epistatic-net

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

Language: Jupyter Notebook - Size: 1.05 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 15 - Forks: 2

lorinanthony/MAPIT

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

Language: C++ - Size: 65.4 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 3

wtaisner/genetic-programming

Estimating epistasis in trees for genetic programming problems

Language: Jupyter Notebook - Size: 8.22 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

insilico/npdr

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

Language: R - Size: 24 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 12 - Forks: 6

Zhengtong-Liu/CS-M226-Project

Non-linear Genetic Effects for Complex Traits

Language: Jupyter Notebook - Size: 22.6 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

colbyford/parEBEN

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

Language: C - Size: 107 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 2

alexcis95/VARI3

Approach to VARIantVARIant interaction through VARIable thresholds and hypothesis testing. VARI3 automates the selection and analysis of the most promising SNPs to identify epistasis.

Language: R - Size: 92.8 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0