Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files
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Updated
Jan 20, 2021 - Python
Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files
Data analysis on natural movement of the population in Romania
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.
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.
Genetic Ancestry
Binary trait Resampling method Adjusting for Sample Structure
Plague Global Phylogeny Manuscript
Collection of materials for teaching about autoencoders
STAT488 - Multivariate Statistics final project at Loyola University Chicago
Crowdfunding Data Analysis
STRUCTURE and ROLLOFF reimplementations for CS 4775 (Computational Genetics and Genomics)
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.
Imputation and Admixture for lcWGS in one goal
Repository for paper looking at phenotypic differences among F1 and F2 oysters from 3 populations in Puget Sound, WA.
Scripts and notes related to the manuscript: Stuart KC & Cardilini APA 2021 Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species. Molecular Ecology 30(6):1419-1434, doi.org/10.1111/mec.15601 † joint first author ‡ joint last author.
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