GitHub topics: admixture
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: 16 days ago - Pushed at: over 1 year ago - Stars: 148 - Forks: 37
DarkEyes/ipADMIXTURE
A data clustering package based on admixture ratios (Q matrix) of population structure analysis.
Language: R - Size: 2.66 MB - Last synced at: 20 days ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1
royfrancis/pophelperShiny
Interactive interface for pophelper using shiny web framework.
Language: R - Size: 2.5 MB - Last synced at: 21 days ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 0
mahui-cn/weapp-ancestry
Ancestry Calculator for WeGene, It features population admixture model and MLE (Maximum Likelihood Estimation) algorithm to estimate admixture.
Language: Python - Size: 6.28 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
jitang-github/asegrm
A genealogy-based method to estimate the GRM within one ancestry in admixed populations
Language: Python - Size: 25.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - 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: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
Zilong-Li/phaseless
Imputation and Admixture for lcWGS in one goal
Language: C++ - Size: 12.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0
AI-sandbox/neural-admixture
Rapid population clustering with autoencoders
Language: Python - Size: 1.61 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 52 - Forks: 8
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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 31 - Forks: 5
jgeofil/mycorrhiza-algorithm
Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data
Language: Python - Size: 15 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 2
NovembreLab/eems-around-the-world
Repo to analyze population genetic data with many different methods
Language: R - Size: 9.92 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 14 - Forks: 8
mpieva/admixr Fork of bodkan/admixr
An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.
Language: R - Size: 8.39 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
TheSergeyPixel/Diablo_G25
Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.
Language: Python - Size: 15.4 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
OpenMendel/ADMIXTURE.jl
Julia wrapper of the ADMIXTURE program for estimating ancestry
Language: Julia - Size: 155 KB - Last synced at: 16 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0
cgplab/PAMES
Tool to estimate purity of tumor samples exploiting DNA Methylation data
Language: R - Size: 165 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 8
btmartin721/makePopMap
Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files
Language: Python - Size: 50.8 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1
asthmacollaboratory/sage-geuvadis-predixcan 📦
Analysis of transcriptome imputation using paired genotype-expression data from SAGE and GEUVADIS
Language: R - Size: 7.44 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1
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: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1
hellenthal-group-UCL/fastGLOBETROTTER
faster haplotype-based admixture inference and dating software
Language: R - Size: 7.61 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 1
nicocriscuolo/StructuRly
Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis
Language: R - Size: 8.89 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 16 - Forks: 8
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.
Language: OpenEdge ABL - Size: 55.8 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 0
esohkevin/gwas-tips
tips and tricks in genome-wide association studies - a tutorial
Size: 19.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 8
baslare/misc
Miscellaneous scripts that do not really deserve their own repos
Language: Jupyter Notebook - Size: 1.65 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
acostauribe/TANGL
Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"
Language: Shell - Size: 1.96 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 3
Tom-Jenkins/admixture_pie_chart_map_tutorial
Tutorial for visualising admixture on a map
Language: R - Size: 704 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 7
mathilab/PRS_Height_Admixed_Populations
Investigating the lack of transferability of polygenic risk scores for height in admixed individuals, using summary statistics from UK Biobank (British) individuals and testing on individuals with admixed ancestry from the Jackson Heart Study, Women's Health Initiative, and Health and Retirement Study.
Language: R - Size: 101 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3
hellenthal-group-UCL/GLOBETROTTER
haplotype-based admixture inference and dating software
Language: R - Size: 2.04 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 3
veeara282/cs4775-structure-rolloff
STRUCTURE and ROLLOFF reimplementations for CS 4775 (Computational Genetics and Genomics)
Language: Python - Size: 3.55 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
ANGSD-wrapper/angsd-wrapper
Utilities for analyzing next generation sequencing data.
Language: Shell - Size: 13.4 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 13 - Forks: 4
btmartin721/phylip2eigenstrat
Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile
Language: Python - Size: 238 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1
btmartin721/bash_scripts
Random bash scripts for working on the AHPCC cluster and for processing input and output files for various programs
Language: Shell - Size: 13.7 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
KamilSJaron/Conjunction
Simulator of secondary CONtact using Fisher's JUNCTION representation of genome admixture.
Language: C++ - Size: 468 KB - Last synced at: 5 months ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 2
