epistasis

There are 0 repository under epistasis topic.

harmslab / epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
genotype-phenotype-maps python epistasis high-order nonlinear modeling genetics evolution
Language:Python 32
Chester75321 / GenEpi
A package for detecting epistasis by machine learning
machine-learning gwas epistasis
Language:Python 20
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).
deep-learning epistasis protein-function-prediction sparse-recovery
Language:Jupyter Notebook 15
lorinanthony / MAPIT
Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)
epistasis epistasis-analysis linear-mixed-models variance-components heritability gwas gwas-tools gwas-case-control genetics
Language:C++ 13
insilico / npdr
NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model
relief glm covariates nearest-neighbors epistasis feature-selection gene-expression genome-wide-data projected-distances gwas eqtl rna-seq
Language:R 12
lcrawlab / i-LDSC
Code and simulations using interaction-LD score regression
epistasis gwas gwas-summary-statistics gwas-tools heritability heritability-estimation ld-score-regression
Language:Python 9
mvMAPIT
lcrawlab / mvMAPIT
The multivariate MArginal ePIstasis Test
epistasis mapit mvmapit r variance-components cpp cran epistasis-analysis gwas gwas-tools linear-mixed-models
Language:R 9
harmslab / notebooks-nonlinear-high-order-epistasis
Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"
epistasis high-order-epistasis statistics genetics jupyter-notebooks genotype-phenotype-maps
Language:Jupyter Notebook 6
colbyford / parEBEN
Parallel Implementations of the Empirical Bayesian Elastic Net Cross-Validation in R
epistasis r regularization bayesian-inference genomics epistasis-analysis qtl-mapping cross-validation regression-models elastic-nets parallel algorithm
Language:C 5
greenelab / model-free-data
Case-control genetics datasets evolved to be epistatic
biodata-mining simulation epistasis snps genetics dataset moore-lab open-data supplement notebook
Language:PostScript 5
harmslab / gpseer
A tool to predict missing data in sparsely sampled genotype-phenotype maps
epistasis genotype-phenotype-map evolution prediction statistics python
Language:Python 5
biolab / red
Inference of Epistatic Gene Networks
network-inference epistasis genetic-interactions mutant-data
Language:Python 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.
black-box-benchmarking discrete-mathematics combinatorial-optimization epistasis non-separability neutrality multi-objectivity ruggedness fitness-landscape benchmark benchmark-problem deterministic noise experiments local-search hill-climber evolutionary-algorithm random-walk multi-objective
Language:Java 3
bglezseoane / pytoxo
A Python tool to calculate penetrance tables for high-order epistasis models
penetrance-tables epistasis full-genome human-genome python genetics bioinformatics
Language:Python 2
UDC-GAC / mpi3snp
GWAS third-level epistatic search tool for cluster architectures
gwas snp snp-genotyping bioinformatics mpi threading parallelism cuda gpu epistasis
Language:C++ 2
pecanka / epidetector
EpiDetector: A tool for identifying epistasis
software epistasis two-stage testing genetics snps efficient fortran
Language:Fortran 1
UDC-GAC / toxo
A library for calculating penetrance tables of any bivariate epistasis model.
epistasis model marchini interaction-effect heritability prevalence penetrance-table snp simulation
Language:MATLAB 1
xsitarcik / epiBAT
epistasis bat-algorithm
Language:Python 1
Zhengtong-Liu / CS-M226-Project
Non-linear Genetic Effects for Complex Traits
bioinformatics epistasis genetics machine-learning
Language:Jupyter Notebook 1
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.
epistasis
Language:R 0
sariya / CUMC_taub
epistasis imputation microarrays wgs structural-variation local-ancestry haplotype-blocks kinship merge plotting
Language:R 0
wtaisner / genetic-programming
Estimating epistasis in trees for genetic programming problems
epistasis epistasis-analysis genetic-programming
Language:Jupyter Notebook 0
Zsailer / notebooks-nonlinear-high-order-epistasis
All materials and analysis as Jupyter notebooks for Genetics paper.
genetics epistasis jupyter-notebook high-order statistics
Language:Jupyter Notebook