David-Peede

anc-der-intro-proj

BIOL1435

Resources for Brown University's BIOL 1435 course.

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

gist-hub

Random assortment of one personal gists and one-liners that I can't seem to remember...

hg19_aa_calls

Code to convert Hg19 reference/alternative alleles to ancestral/derived alleles.

hog-peanut-morphometrics

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.

smc-working-group

David-Peede/BIOL1435

Resources for Brown University's BIOL 1435 course.

David-Peede/hog-peanut-morphometrics

David-Peede/smc-working-group

David-Peede/anc-der-intro-proj

David-Peede/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/David-Peede.github.io

Personal website.

David-Peede/gist-hub

Random assortment of one personal gists and one-liners that I can't seem to remember...

David-Peede/hg19_aa_calls

Code to convert Hg19 reference/alternative alleles to ancestral/derived alleles.

David-Peede/MUC19

Code associated with Villanea and Peede et. al. 202X.

David-Peede/RIPTA

Package to calculate site pattern based summary statistics described in Peede et al. 202X.

David-Peede/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.

David-Peede/evo-gen-tutorials

David-Peede/iA-Writer-Template

My iA Writer template.

David-Peede/Introgression-detection

David-Peede/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.

David-Peede/mentee_research

David-Peede/ppg

Plasmodium Pop-Gen

David-Peede/santomea_natural_history

Code associated with Peede et al 202X

David-Peede/ShellScripts

A random assortment of shell scripts.

David-Peede/targt_pipeline_vcf

Code associated with Pierini et al 202X.