Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

Data analysis on natural movement of the population in Romania

Repository for "Hybridization and inbreeding affect the survival of a critically endangered coral"

Binary trait Resampling method Adjusting for Sample Structure

Plague Global Phylogeny Manuscript

STRUCTURE and ROLLOFF reimplementations for CS 4775 (Computational Genetics and Genomics)

Repository for code used in the study "Patterns of population structure and complex haplotype sharing at continental and local scales in field isolates of the green alga Chlamydomonas reinhardtii"

BIOI500 - Advanced Bioinformatics final project at Loyola University Chicago.

Collection of materials for teaching about autoencoders

STAT488 - Multivariate Statistics final project at Loyola University Chicago

Crowdfunding Data Analysis

A Snakemake powered pipeline developed to perform population structure and admixture analysis given multiple Variant Call Format datasets. This has been developed in partial fulfilment of a MSc in Bioinformatics at the University of Pretoria by Graeme Ford.

Population Structured Bayesian Epistasis Association Mapping

This repository if for creating auto-encoders easily. The main focus of the auto-encoders on this page is for genetic and spectral data analysis but likely could be used for any high dimensional data

In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples.

Nextflow pipeline for analyzing empirical WGS data for the effect of positive selection on IBD-based inference

GWAS on rice RNA seq data, features use of statgenGWAS, and experimentation with different methods of pop. structure control

Repository for paper looking at phenotypic differences among F1 and F2 oysters from 3 populations in Puget Sound, WA.