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simplepaintpanel

This is a simple paint application programmed in java

slim

Selection on Linked Mutations: A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.

slim_tsbenchmarks

This Repository contains the benchmark simulations to test our implementation of Pedigree Recording.

slimsimulations

Models of Stickleback fish populations in Alaska. Continuous space models simulate a Marine population along a coast and many, much smaller, freshwater populations connected by migration. Plotly website listed to show data

spot-detection

Contains code to simualte spots on background noise, and the convolutional neural network framework to train on those images.

spring_term_paper_bgmp

The source files for a spring 2020 BGMP term paper focused on phip-seq analysis pipeline

squirrelsuiterscripts

This is the C# UNITY scripts to our game, Squirrel Suiter.

stdpopsim

A library of standard simulation models for msprime

sticklebackpaper

LaTeX Source for Stickleback Paper

superrepo-test

test repo for submodule learning

test-sphinx-autobuild

treesequencelearning

Code For learning on Encodings of msprime's TreeSequence Object.

treesequenceprimer

This repository will hold a notebook which will walk through and explain some tskit `TreeSequence` basics

treesequencerecording

This repository contains the pre-print pdf of our published paper _Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes_

treesequencevis

This repository contains the code that will visualize a treeSequence object from tskit

treevis

This repository contains the source code for my latest project where were will be visulaizing genealogical history for use with deep learning.

tsencode

This is the starting code for endcoding an msprime TreeSequence Object into a 3D array for ML and visualization purposes

undergradthesis

contains the source for my undergraduate thesis