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Patrick Monnahan's Projects

ancestry_pipeline icon ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

camara icon camara

code for analysis of camara project

cnv-sim icon cnv-sim

Copy Number Variations (CNV) Simulator

dataprep icon dataprep

start with raw plink, end with standardized QCed plink

ld icon ld

Calculate r2 from unphased allele count files.

odyssey icon odyssey

Odyssey: A semi-automated pipeline for the prepping, cleaning, phasing, imputing, analyzing, and visualizing genomic data

osteocnv icon osteocnv

run CNVkit on germline osteosarcoma trio samples

ploidysim icon ploidysim

Coalescent simulations (using mssel) to compare population genomic footprints of selection across different ploidy levels.

rfmix icon rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2

scantools icon scantools

Collection of tools for selection analysis of genomic data and a wrapper for job submission on slurm cluster

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