EricArcher/strataG

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

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Tom-Jenkins/mapmixture

An R package and web app for spatial visualisation of admixture on a projected map

Language: R - Size: 25 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 31 - Forks: 5

ocbe-uio/rBAPS

R implementation of the BAPS software for Bayesian Analysis of Population Structure

Language: R - Size: 1.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 4

RoshniRanaDS/Excel-Challenge-from-University-Of-Toronto

Crowdfunding Data Analysis

Size: 1.25 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

esteinig/netviewr

Graph decorators for data and population structure visualization :octopus:

Language: R - Size: 2.04 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 2

hwittich/Cow_PCA

STAT488 - Multivariate Statistics final project at Loyola University Chicago

Language: R - Size: 4.42 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

hwittich/Benchmarking_Pop_Structure_Tools

BIOI500 - Advanced Bioinformatics final project at Loyola University Chicago.

Size: 643 KB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

MareesAT/GWA_tutorial

A comprehensive tutorial about GWAS and PRS

Size: 31 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 695 - Forks: 301

V-Z/course-r-mol-data

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

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gtonkinhill/rhierbaps

rhierbaps: R implementation of hierBAPS

Language: R - Size: 1.63 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 30 - Forks: 3

VahidHeidari/StrBEAM

Population Structured Bayesian Epistasis Association Mapping

Language: Python - Size: 651 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

sa-lee/starmie 📦

starmie: plotting and inference for population structure models :star2:

Language: R - Size: 6.3 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 11 - Forks: 6

QTCAT/qtcat

Quantitative Trait Cluster Association Test in R

Language: R - Size: 243 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 24 - Forks: 10

btmartin721/makePopMap

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

Language: Python - Size: 50.8 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

jgeofil/mycorrhiza-article-source

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.

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rorycraig337/Chlamydomonas_reinhardtii_population_structure

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"

Language: Perl - Size: 185 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

royfrancis/pophelper

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

Language: R - Size: 49.7 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 127 - Forks: 35

mkierczak/autoencoders_workshop

Collection of materials for teaching about autoencoders

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esohkevin/CamPopStruct

Fine-scale genetic structure in South Western Cameroon

Language: R - Size: 141 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 1

ahmedmoustafa/genetic-ancestry

Genetic Ancestry

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royfrancis/pophelperShiny

Interactive interface for pophelper using shiny web framework.

Language: R - Size: 2.5 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

bguo068/posseleff_empirical

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

Language: Nextflow - Size: 2.15 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

bguo068/posseleff_simulations

Nextflow pipeline to assess the impact of positive selection on Identity by Descent (IBD)-based inferences, utilizing population genetic simulations and true IBD inferences.

Language: Python - Size: 66.7 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

ktmeaton/plague-global-phylo-paper

Plague Global Phylogeny Manuscript

Language: HTML - Size: 9.22 MB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

Tuks-ICMM/Population-Structure-Workflow

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.

Language: Python - Size: 25.9 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

Zilong-Li/phaseless

Imputation and Admixture for lcWGS in one goal

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Tom-Jenkins/admixture_pie_chart_map_tutorial

Tutorial for visualising admixture on a map

Language: R - Size: 704 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 13 - Forks: 7

Annndruha/vk_community_distribution

vk.com community members sex and age distribution (population pyramid)

Language: Python - Size: 272 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0

joellesophya/BRASS

Binary trait Resampling method Adjusting for Sample Structure

Language: C++ - Size: 2.45 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

solelena/PSReliP

An integrated pipeline for analysis and visualization of Population Structure and Relatedness based on genome-wide genetic variant data

Language: R - Size: 168 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

msesia/knockoffgwas

A flexible tool for the multi-resolution localization of causal variants across the genome, accounting for population structure.

Language: C++ - Size: 136 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 14 - Forks: 0

katarinastuart/Sv1_StarlingGBS

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.

Language: Shell - Size: 30.8 MB - Last synced: 11 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 2

MPB-mrcg/Pfalciparum_Mali_geo_temp_popgen

This study assessed the spatial genetic variation in P. falciparum populations in Mali

Language: R - Size: 8.26 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 1

aangush/Rice-GWAS

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

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justincbagley/piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

Language: Shell - Size: 13.7 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 10 - Forks: 3

Ana-Iordache/SDDA_Project

Data analysis on natural movement of the population in Romania

Language: Python - Size: 156 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

deropi/BathyBrooksiSymbionts

Language: Python - Size: 16.7 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

PAMorin/TESS3r_SNPs

R-markdown script for geographic population genetic structure analysis with Tess3r

Size: 203 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 3 - Forks: 1

DarkEyes/ipADMIXTURE

A data clustering package based on admixture ratios (Q matrix) of population structure analysis.

Language: R - Size: 2.66 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 4 - Forks: 1

veeara282/cs4775-structure-rolloff

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

Language: Python - Size: 3.55 MB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

Zhiwu-Zhang-Lab/genetic_spectral_AutoEncoder

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

Language: Jupyter Notebook - Size: 138 KB - Last synced: 15 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0