andrewkern Goto Github PK

adding-species-manuscript

manuscript materials for the adding species paper

analysis

Analysis of inference methods on standard population models

analysis2

Analysis for the second consortium paper.

analysis2_manuscript

manuscript repo for the paper describing selection additions and analysis

arabidopsis_recomb_maps

Recombination maps for A. thaliana with scripts and documentation

bagels

open source bagel recipe; let's raise the quality of bagels worldwide :bagel: :rocket:

betterbib

:green_book: Update BibTeX files with info from online resources.

bio399

Bio399- Computational Genetics

biol610

intro to programming for IE2 evolution students

dadi-cli

A command line interface for dadi

demes-c

C library for parsing Demes demographic models

demogposseldadiscripts

Scripts for doing demographic inference using Dadi package.

discoal_multipop

placeholder

dispersenn2

estimating dispersal distance from georeferenced polymorphisms

gcn

gdp_pgs

Creating a polygenic score predictor of GDP using Arabidopsis GWAS data

hka

A simple, fast implementation of the Hudson Kreitman Aguadé (1989) test

hyphy

HyPhy: Hypothesis testing using Phylogenies

lavingtonkern

files assocated with Lavington and Kern (2017, to appear)

limix

Linear mixed model for genomic analyses.

locator

deep learning prediction of geographic location from individual genome sequences

machine-learning-book

Code Repository for Machine Learning with PyTorch and Scikit-Learn

manuscript

PopSim consortium manuscript

miscdadiscripts

Various python scripts performing dadi optimization (often using pyOpt's ALPSO)

mktest

McDonald-Kreitman test written in Ruby

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

msprime-1.0-paper

Publication describing msprime 1.0

my_first_repo

learning in BI610

octo_snakemake

workflow for hifiasm assembly stuff

onesiteforward

Simple forward time population genetic simulations of a single site. Useful for learning about sojourn times of alleles destined to fix.