Cheyenne Payne's repositories
CIPRES-notebooks
SDSC CIPRES Jupyter notebooks for phylo tools
cipres_scripts
Scripts useful for processing input/output files related to CIPRES activities
fastastic
Prokaryotic genome assembly, annotation, + quality check
git-novice
Software Carpentry introduction to Git for novices.
gtseq-scripts
Scripts written to streamline Palumbi lab multiplexing data analysis, which uses the GTseq-Pipeline to produce genotypes (https://github.com/GTseq/GTseq-Pipeline#gtseq-pipeline).
jese4sci-FP
Final Project track of the jese4sci short course
mitonucABC
Uses an ABC framework to estimate selection coefficients against mitonuclear incompatibilities by simulating admixed populations.
thermotolerance
Scripts used for QTL mapping, differential gene expression, WGCNA coexpression, etc analyses in Payne et al 2021.
jese4sci.instructors
Instructor material for the jese4sci course
OpenByDesign
A guide to doing open and reproducible science at Stanford
palumbi_scripts
Random scripts used to process data in the Palumbi lab @hopkinsmarinestation http://palumbi.stanford.edu/
QTLmapping_CTmax
Contains QTL mapping pipeline used to map CTmax QTL in Xiphophorus F2s in Payne et al 2021.
shell-novice
Software Carpentry introduction to the shell for novices.
swordtail-offspring-size
Scripts and data for generating figures that appear in Payne et al 2023, "Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails"
thermtol_wgcna
Pipeline to create gene co-expression networks with WGCNA, run GO enrichment, and permute expected distributions of genes with F1 misexpression from RNAseq data.