Interactive interface for pophelper using shiny web framework.
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Updated
Dec 29, 2020 - R
Interactive interface for pophelper using shiny web framework.
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.
Miscellaneous scripts that do not really deserve their own repos
Random bash scripts for working on the AHPCC cluster and for processing input and output files for various programs
Julia wrapper of the ADMIXTURE program for estimating ancestry
An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.
R scripts that use Shiny to render interactive popgen plots
Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"
STRUCTURE and ROLLOFF reimplementations for CS 4775 (Computational Genetics and Genomics)
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-li…
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"
Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile
A data clustering package based on admixture ratios (Q matrix) of population structure analysis.
Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files
faster haplotype-based admixture inference and dating software
Analysis of transcriptome imputation using paired genotype-expression data from SAGE and GEUVADIS
Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data
Simulator of secondary CONtact using Fisher's JUNCTION representation of genome admixture.
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