David Peede's repositories
chimp_maf_to_vcf
Code to convert hg19.panTro6.synNet.maf.gz to an all sites VCF file where the only indiviual is panTro6 and is homozygous at every site. You can download the .maf file from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro6/hg19.panTro6.synNet.maf.gz
David-Peede.github.io
My personal website.
gist-hub
Random assortment of one personal gists and one-liners that I can't seem to remember...
MUC19
Code associated with Villanea and Peede et. al. 202X.
RIPTA
Package to calculate site pattern based summary statistics described in Peede et al. 202X.
Dplus
Code for "Leveraging shared ancestral variation to detect local introgression" Lesly Lopez Fang, David Peede, Diego Ortega Del-Vecchyo, Emily Jane McTavish and Emilia Huerta-Sanchez.
iA-Writer-Template
My iA Writer template.
MatuteLabProtocols
Various protocols that worked best for me during my time in the Matute Lab in tex and pdf format for the posterity of the Matute Lab. Please contact me with any questions or clarifications, and I will be happy to update the documents as needed for clarity.
ppg
Plasmodium Pop-Gen
ShellScripts
A random assortment of shell scripts.
targt_pipeline_vcf
Code associated with Pierini et al 202X.