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Max Winston's Projects

abs_corr icon abs_corr

Scripting to create an absence-presence matrix (APM) from GBS data. Specifically, take the output of pyRAD (.loci and .stats file), and create a APM and sample output files

dadi icon dadi

Repository for scripts to generate allele frequency spectrum from pyRAD output file (Eaton, 2014) and test competing a priori models using the Diffusion Approximation for Demographic Inference (dadi)

fst icon fst

Basic R Script to take .usnps.geno file generated by pyRAD, compute the Fst values across a two-pop sample, and compare to a null sample.

g-phocs icon g-phocs

Repository for implementation of Generalized Phylogenetic Coalescent Sampler (G-PhoCS)

in_silico icon in_silico

In silico digestion of genomes with restriction enzymes (focus on ApeK1)

morpho icon morpho

Repository for all shape analysis related code

node_calibration icon node_calibration

Simple codes for using a cross-validation technique on Sanderson's penalized likelihood method implemented in chronos (R)

qiime icon qiime

Scripts used for Cannabis microbiome project (Winston et al., 2014: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099641)

stat302 icon stat302

notes from my 302 class on Bayesian methods and principles of statistics

stat_gen_labs icon stat_gen_labs

Labs I wrote for Introduction to Statistical Genetics (HGEN47100) with John Novembre, Brandon Pierce, and Lin Chen

technical_replicates icon technical_replicates

This is a simple python script which takes in a two-sample unlinked_snps file from pyRAD (technical replicates) to evaluate genotype accuracy. The outputs are the location of the snps in the larger unlinked_snps file, and then a binary matching score.

utility icon utility

Collection of scripts (Python and R) to accomplish miscellaneous tasks

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