yuqingc7/NYC-oyster-admixture

This repository contains scripts for NYC oyster admixture project

Language: R - Size: 102 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

EricArcher/strataG

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

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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 at: 27 days ago - Pushed at: about 2 years ago - Stars: 151 - Forks: 37

esteinig/netviewr

Mutual nearest neighbor graphs for population structure inference and visualization :octopus:

Language: Rust - Size: 2.1 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 18 - Forks: 2

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.

Language: TeX - Size: 1.46 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 4

justincbagley/piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

Language: Shell - Size: 13.7 MB - Last synced at: 8 days ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 3

gtonkinhill/rhierbaps

rhierbaps: R implementation of hierBAPS

Language: R - Size: 1.63 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 35 - Forks: 3

DarkEyes/ipADMIXTURE

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

Language: R - Size: 2.67 MB - Last synced at: 5 days ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1

bonifazi/labradoR

An R Package To Read, Process, and Visualize Retriever's Output.

Language: R - Size: 1.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 1

Tom-Jenkins/mapmixture

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

Language: R - Size: 28.7 MB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 44 - Forks: 7

royfrancis/pophelperShiny

Interactive interface for pophelper using shiny web framework.

Language: R - Size: 2.5 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 0

ocbe-uio/rBAPS

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

Language: R - Size: 1.02 MB - Last synced at: 8 days ago - Pushed at: 8 months ago - Stars: 10 - Forks: 5

wilsonfrantine/ggDAPC

A set of codes to help plot Discriminant Analysis of Principal Components from Adegenet R package

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ahmedmoustafa/genetic-ancestry

Genetic Ancestry

Language: Jupyter Notebook - Size: 15.3 MB - Last synced at: 4 days ago - Pushed at: 9 months ago - Stars: 1 - 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 at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - 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 at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

RoshniRanaDS27/Crowd_Funding_Data_Analysis_by_Excel

Crowdfunding Data Analysis

Size: 783 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Zilong-Li/phaseless

Imputation and Admixture for lcWGS in one goal

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AIHAgreda/helioseris_ddrad

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

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hwittich/Cow_PCA

STAT488 - Multivariate Statistics final project at Loyola University Chicago

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hwittich/Benchmarking_Pop_Structure_Tools

BIOI500 - Advanced Bioinformatics final project at Loyola University Chicago.

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MareesAT/GWA_tutorial

A comprehensive tutorial about GWAS and PRS

Size: 31 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 695 - Forks: 301

VahidHeidari/StrBEAM

Population Structured Bayesian Epistasis Association Mapping

Language: Python - Size: 651 KB - Last synced at: almost 2 years ago - Pushed at: about 4 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 at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 11 - Forks: 6

QTCAT/qtcat

Quantitative Trait Cluster Association Test in R

Language: R - Size: 243 KB - Last synced at: almost 2 years ago - Pushed at: over 4 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 at: almost 2 years ago - Pushed at: over 4 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 at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 1

annndruha/vk_community_distribution 📦

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

Language: Python - Size: 272 KB - Last synced at: 8 months ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 1

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 at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Tom-Jenkins/admixture_pie_chart_map_tutorial

Tutorial for visualising admixture on a map

Language: R - Size: 704 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 7

joellesophya/BRASS

Binary trait Resampling method Adjusting for Sample Structure

Language: C++ - Size: 2.45 MB - Last synced at: 9 months ago - Pushed at: over 2 years 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 at: over 2 years ago - Pushed at: over 2 years 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.

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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 at: over 2 years ago - Pushed at: about 5 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 at: over 2 years ago - Pushed at: about 3 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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Ana-Iordache/SDDA_Project

Data analysis on natural movement of the population in Romania

Language: Python - Size: 156 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

deropi/BathyBrooksiSymbionts

Language: Python - Size: 16.7 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

ktmeaton/plague-global-phylo-paper

Plague Global Phylogeny Manuscript

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PAMorin/TESS3r_SNPs

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

Size: 203 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 1

veeara282/cs4775-structure-rolloff

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

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ksil91/PS-Oly-Larvae-Growth

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

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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

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