population-structure

There are 4 repositories under population-structure topic.

• MareesAT / GWA_tutorial

  A comprehensive tutorial about GWAS and PRS

  bioinformaticsgeneticsgenomicsgwasplinkpopulation-stratificationpopulation-structureprsqcrunix
  787
• pophelper

  royfrancis / pophelper

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

  population-geneticsrpopulation-structureadmixturefaststructureclumppdistruct
  Language:R 136

• Tom-Jenkins / mapmixture

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

  admixtureancestrymapmixturepopulation-structurershiny
  Language:R 37

• gtonkinhill / rhierbaps

  rhierbaps: R implementation of hierBAPS

  population-geneticspopulation-genomicspopulation-structurer
  Language:R 33

• QTCAT / qtcat

  Quantitative Trait Cluster Association Test in R

  population-structuregwas
  Language:R 25

• EricArcher / strataG

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

  population-structurelocus-summariespopulation-geneticspopulation-genomicsgeneticssnpssnp-datadna-sequencesmicrosatellites
  Language:HTML 24

• Tom-Jenkins / admixture_pie_chart_map_tutorial

  Tutorial for visualising admixture on a map

  radmixturepie-chartggplot2population-structure
  Language:R 23

• msesia / knockoffgwas

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

  causal-variantspopulation-structureuk-biobankgwas
  Language:C++ 14

• sa-lee / starmie

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

  population-genomicspopulation-geneticspopulation-structurerdata-visualization
  Language:R 12

• justincbagley / piranha

  Scripts for file processing and analysis in phylogenetics and phylogeography

  phylogenyphylogeographyshellrbayesian-inferencemaximum-likelihoodsnpspopulation-structuresupercomputerssh
  Language:Shell 11

• ocbe-uio / rBAPS

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

  bayesian-analysisr-packagepopulation-structure
  Language:R 10

• 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.

  rmolecular-biologymolecular-evolutioncourselearningscriptsscriptingdata-analysisdata-visualizationmolecular-databioconductorphylogeneticsphylogenetic-treesphylogenypopulation-geneticspopulation-genomicspopulation-structurebiogeographyphylogeographyevolution
  Language:TeX 8

• esteinig / netviewr

  Graph decorators for data and population structure visualization :octopus:

  graphspopulation-geneticspopulation-structurertidyverse
  Language:R 6

• solelena / PSReliP

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

  data-visualizationpopulation-structurerelatednessplinkplink2shiny-appsgenome-analysis
  Language:R 6

• annndruha / vk_community_distribution

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

  vk-apisociologypopulationpopulation-structurevkontaktevkontakte-api
  Language:Python 5

• DarkEyes / ipADMIXTURE

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

  admixturebioinformaticsdata-clustering-algorithmpopulation-stratificationpopulation-structurer
  Language:R 4

• royfrancis / pophelperShiny

  Interactive interface for pophelper using shiny web framework.

  population-geneticspopulation-structurepophelperstructureadmixturefaststructure
  Language:R 4

• PAMorin / TESS3r_SNPs

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

  rtesspopulation-structurespatial-analysis
  3

• MPB-mrcg / Pfalciparum_Mali_geo_temp_popgen

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

  population-geneticsdrug-resistancepopulation-structure
  Language:R 2
• Rice-GWAS

  aangush / Rice-GWAS

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

  geneticsgenomicsgwaspopulation-structurerna-seqstatgengwaskinship
  Language:HTML 1

• bguo068 / posseleff_empirical

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

  deconvolutioneffective-population-sizeempirical-dataibd-inferenceimputationinfomapmultiple-infectionplasmodium-falciparumpopulation-structureposseleff-paperwhole-genome-sequencingmetadata
  Language:Nextflow 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.

  effective-population-sizeidentity-by-descentpopulation-structurepositive-selectionposseleff-papertrue-ibdibd-based-inferencespopulation-genetic-simulationsnextflow-pipeline
  Language:Python 1

• esohkevin / CamPopStruct

  Fine-scale genetic structure in South Western Cameroon

  popgenpopulation-structuregwas
  Language:R 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.

  machine-learningpopulation-geneticsphylogeneticsdimensionality-reductionsnpsinvasive-speciespopulation-structurepredictive-modeling
  Language:TeX 1

• 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.

  genomicsinvasive-speciesoutlier-analysispopulation-geneticspopulation-structurerapid-adaptation
  Language:Shell 1

• ksil91 / PS-Oly-Larvae-Growth

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

  marine-biologyoystersphenotypepopulation-structure
  Language:PostScript 1

• Zilong-Li / phaseless

  Imputation and Admixture for lcWGS in one goal

  genotype-imputationlow-coverage-sequencingpopulation-structurepopulation-geneticsbioinformatics
  Language:C++ 1

• Ana-Iordache / SDDA_Project

  Data analysis on natural movement of the population in Romania

  data-analysis-pythonpopulation-structureromanianatural-movement
  Language:Python 0

• hwittich / Benchmarking_Pop_Structure_Tools

  BIOI500 - Advanced Bioinformatics final project at Loyola University Chicago.

  1000genomesbenchmarking-studypcaplinkpopulation-structurebashpythonr
  0

• hwittich / Cow_PCA

  STAT488 - Multivariate Statistics final project at Loyola University Chicago

  pcaphylogeneticspopulation-structurer
  Language:R 0

• RoshniRanaDS / Crowd_Funding_Data_Analysis_by_Excel

  Crowdfunding Data Analysis

  column-generationconditional-formattingpivot-tablesstacked-column-chartsstatistical-analysiswritten-reportcrowfunding-goal-analysisdate-created-conversiondate-ended-conversionpivot-tables-and-line-graphscentral-tendencyif-conditionscolumnsplittermeanmedianpopulation-structurestandard-deviationstastical-analysis-toolsvarianceexcel
  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.

  admixturegeneticspopulation-structuresnakemakeworkflow
  Language:Python 0

• VahidHeidari / StrBEAM

  Population Structured Bayesian Epistasis Association Mapping

  beamstructuregeneticsgwaspopulation-structurebayesian-inferencevariational-inferenceassociation-mappingmachine-learning
  Language:Python 0
• genetic-ancestry

  ahmedmoustafa / genetic-ancestry

  Genetic Ancestry

  ancestrydiversityethnicity-analysisgenomicsggplotpcaplinkpopulation-geneticssingle-nucleotide-polymorphismspopulation-structureprincipal-component-analysis
  Language:Jupyter Notebook

• ktmeaton / plague-global-phylo-paper

  Plague Global Phylogeny Manuscript

  plaguephylogeneticsphylodynamicsphylogeographypopulation-structure
  Language:HTML

• pommevilla / sbfp

  biofilmbioinformaticsfeature-selectionkmer-countingmachine-learningpopulation-structuresalmonellasnakemakexgboost
  Language:Python