McVean Lab's repositories
treeseq-inference
Work for the tree sequence inference paper.
TreeWASDir
Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.
DEploid
dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
tskit-workshop
JupyterHub infrastructure for tskit workshops
DEploid-r
An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
schmidtWorkshop
Code used in Scmidt Science Fellowship workshop
mixedIBD-Supplement
Supplementary material for mixedIBD paper
schmidtWorkshop-docker
Builds a docker image out of the schmidtWorkshop repo