admixture

There are 2 repositories under admixture topic.

• pophelper

  royfrancis / pophelper

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

  population-geneticsrpopulation-structureadmixturefaststructureclumppdistruct
  Language:R 136

• AI-sandbox / neural-admixture

  Rapid population clustering with autoencoders

  machine-learninggenomicsadmixtureancestry-inferencepopulation-genetics
  Language:Python 53

• Tom-Jenkins / mapmixture

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

  admixturershinypopulation-structuremapmixtureancestry
  Language:R 35

• Tom-Jenkins / admixture_pie_chart_map_tutorial

  Tutorial for visualising admixture on a map

  admixtureggplot2pie-chartpopulation-structurer
  Language:R 23

• nicocriscuolo / StructuRly

  Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis

  structureadmixtureqtablesbarplotsshinytriangleplotplotlypopulation-analysisinteractive-plotshierarchic-analysiscomparing-partitions
  Language:R 19

• NovembreLab / eems-around-the-world

  Repo to analyze population genetic data with many different methods

  population-geneticsdata-visualizationprinciple-component-analysisstructureadmixturesnakemake-workflow
  Language:R 15

• ANGSD-wrapper / angsd-wrapper

  Utilities for analyzing next generation sequencing data.

  softwarengs-analysisngsvisualizationguirbashshellwrapperpopulation-geneticsnext-generation-sequencingsfsbam-filesfastagenotype-likelihoodsthetasinbreeding-coefficientadmixtureuser-friendly
  Language:Shell 14
• gwas-tips

  esohkevin / gwas-tips

  tips and tricks in genome-wide association studies - a tutorial

  gwasgwas-toolsgwas-pipelinegwas-datasetthesissnptestplinkqctoolimpute2shapeit2admixturegenotype-datachromopainterfinestructurevcftools
  13

• cgplab / PAMES

  Tool to estimate purity of tumor samples exploiting DNA Methylation data

  epigenomicsdna-methylationadmixturepuritytumor
  Language:R 10

• hellenthal-group-UCL / fastGLOBETROTTER

  faster haplotype-based admixture inference and dating software

  bioinformaticsgenomicsadmixture
  Language:R 8

• jgeofil / mycorrhiza-algorithm

  Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data

  mycorrhizasplitstreeancestrypopulation-geneticsphylogeneticsmachine-learningstructureadmixturerandom-forestsdimensionality-reductionmultilocus-genotype-dataanalysis
  Language:Python 6
• ENAH_curso_aDNA_2019

  mnievesc / ENAH_curso_aDNA_2019

  This repository contains practical data analyses exercises for the special course on Paleogenomics and Anthropology held at the National School of Anthropology of Mexico (ENAH), May 6 to 10, 2019. Topics include performing QC on aDNA NGS data, assigning mtDNA haplogroups and testing hypotheses w/PCA and ADMIXTURE analyses. No previous command-line experience needed.

  admixtureancientdnabammtdnapcateaching-materialstutorial
  Language:OpenEdge ABL 6

• OpenMendel / ADMIXTURE.jl

  Julia wrapper of the ADMIXTURE program for estimating ancestry

  openmendeladmixture
  Language:Julia 6

• DarkEyes / ipADMIXTURE

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

  admixturepopulation-structurepopulation-stratificationdata-clustering-algorithmrbioinformatics
  Language:R 4

• hellenthal-group-UCL / GLOBETROTTER

  haplotype-based admixture inference and dating software

  bioinformaticsgenomicsadmixture
  Language:R 4

• royfrancis / pophelperShiny

  Interactive interface for pophelper using shiny web framework.

  population-geneticspopulation-structurepophelperstructureadmixturefaststructure
  Language:R 4

• TheSergeyPixel / Diablo_G25

  Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.

  23andmeadmixtureancestrypythonvcfconvertergatk
  Language:Python 4

• acostauribe / TANGL

  Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"

  genomicsphasingancestryibdadmixturepca-analysis
  Language:Shell 3

• asthmacollaboratory / sage-geuvadis-predixcan

  Analysis of transcriptome imputation using paired genotype-expression data from SAGE and GEUVADIS

  predixcanadmixturestatistical-geneticstwas
  Language:R 2

• btmartin721 / phylip2eigenstrat

  Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

  admixtoolsadmixtured-statisticddradddrad-sequencingeigenstratf-statisticsgenohybridizationindintrogressionphylippopulation-geneticspopulation-genomicspyradradrad-sequencingsnps
  Language:Python 2

• baslare / misc

  Miscellaneous scripts that do not really deserve their own repos

  xgboostadmixtureairbnbpaper-reproductioncitizen-sciencepopulation-genetics
  Language:Jupyter Notebook 1

• epsalazarf / PopGenRShiny

  R scripts that use Shiny to render interactive popgen plots

  bioinformaticspopulation-genomicspopulation-geneticsadmixturepcaplots-in-r
  Language:R 1

• KamilSJaron / Conjunction

  Simulator of secondary CONtact using Fisher's JUNCTION representation of genome admixture.

  simulatorgenome-admixturesecondary-contacthybrid-zoneadmixturebiologypopulation-genetics
  Language:C++ 1

• btmartin721 / makePopMap

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

  admixturehybridizationintrogressionpedigreephylipplink-filespopmappopulation-geneticspopulation-genomicspopulation-structurestructurestructure-file
  Language:Python 0

• 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"

  population-geneticspopulation-structureadmixtureidentity-by-descent
  Language:Perl 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

• veeara282 / cs4775-structure-rolloff

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

  computational-geneticsgenomicspopulation-geneticspopulation-structureadmixture
  Language:Python 0

• btmartin721 / bash_scripts

  Random bash scripts for working on the AHPCC cluster and for processing input and output files for various programs

  admixturebashbash-scriptpbs-scriptpyradstructure
  Language:Shell

• mcol / admixmap

  A program to model admixture using marker genotype data

  admixturegenetics
  Language:C++

• mpieva / admixr

  An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.

  rrstatsbioinformaticsbioconductoradmixturegenomics
  Language:R

• TauConsortium / TANGL

  Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"

  admixturealzheimers-diseasepopulation-genetics
  Language:Shell