This repository contains all code and data files used to perform QTL mapping and gene expression and co-expression analyses to study the underlying genomic architecture of thermotolerance in swordtails, most recently published in Payne et al 2022.
-
QTL mapping scripts
- Pipeline for mapping critical thermal maximum (CTmax) QTL for artificial X. malinche x X. birchmanni hybrids.
-
Expression analysis scripts
- Scripts used to perform differential gene expression analysis with tissue-level RNAseq data obtained from an ambient vs thermal stress experiment with X. malinche, X. birchmanni, and F1 hybrids.
-
ThermTol WGCNA analysis scripts
- Scripts used to create and explore gene co-expression networks for brain and liver RNAseq thermal stress experiment data.
-
input files
- All data files required to run all scripts contained in this repository and reproduce analyses in Payne et al 2022.
Questions and suggested improvements are greatly appreciated - please reach out to the repository owner at cypayne at stanford dot edu.