Kern-Ralph CoLab
Repositories associated with the collaborary research group of Andrew Kern and Peter Ralph
University of Oregon
Pinned Repositories
diploSHIC
feature-based deep learning for the identification of selective sweeps
discoal
discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples
disperseNN
Estimating dispersal using deep neural networks
FILET
Software for detecting introgression using supervised machine learning
locator
deep learning prediction of geographic location from individual genome sequences
mapNN
neural network for estimating demographic maps from SNPs
popvae
genotype dimensionality reduction with a VAE
ReLERNN
Recombination Landscape Estimation using Recurrent Neural Networks
shIC
The Soft/Hard Inference through Classification tool for detecting hard and soft selective sweeps
spaceness
Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
Kern-Ralph CoLab's Repositories
kr-colab/diploSHIC
feature-based deep learning for the identification of selective sweeps
kr-colab/ReLERNN
Recombination Landscape Estimation using Recurrent Neural Networks
kr-colab/discoal
discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples
kr-colab/locator
deep learning prediction of geographic location from individual genome sequences
kr-colab/popvae
genotype dimensionality reduction with a VAE
kr-colab/FILET
Software for detecting introgression using supervised machine learning
kr-colab/shIC
The Soft/Hard Inference through Classification tool for detecting hard and soft selective sweeps
kr-colab/spaceness
Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
kr-colab/disperseNN
Estimating dispersal using deep neural networks
kr-colab/mapNN
neural network for estimating demographic maps from SNPs
kr-colab/stairwayPlotMisorient
Liu and Fu's StairwayPlot program modified to estimate a mispolarization parameter
kr-colab/colab_wiki
kr-colab/disperseNN2
estimating dispersal distance from georeferenced polymorphisms
kr-colab/spatial_sims_standard
standardizing spatial simulation slim scripts with a template
kr-colab/im_clam
package for exact calculation of the joint site frequency spectrum under Isolation with Migration models as described in Kern and Hey (2017) http://www.genetics.org/content/207/1/241
kr-colab/product-space-FEM
kr-colab/greatapes_sims
kr-colab/bio610_popgen
Bio 610 module on population genetics
kr-colab/msUtils
A collection of C utilities for working with ms-formatted output files. Code is fast, flexible, and has many stats implemented
kr-colab/popCons
constrained elements predicted from population genomic data
kr-colab/popgenDL_crashcourse
kr-colab/snakemake_example
snakemake workflow example for msprime
kr-colab/softShoulders
Contains supplementary data from the Schrider et al. (2015) "Soft Shoulders" paper.