This repository contains the code written by Maria Carilli to run analysis of cis and trans regulatory differences between homozygous strains using RNA-seq data from parents of both strains and their hybrid crosses, as well as code to visualize the results. It requires that replicates are available.
- Source code is in the
R/directory. - Example vignettes for single-condition or multiple-condition regulation are available in the
vignettes/directory.
A Python port of XgeneR is available: see XgenePy.
XgeneR can be installed in R with the following command:
devtools::install_github("pachterlab/XgeneR")The XgeneR method is described in
Ingileif B. Hallgrímsdóttir, Maria Carilli, Lior Pachter, Estimating cis and trans contributions to differences in gene regulation, bioRxiv, 2024, doi.org/10.1101/2024.07.13.603403.