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.
The preprint "Estimating cis and trans contributions to differences in gene regulation" (Hallgrímsdóttir et al., 2024) describes the theory behind the model, statistical tests, and visualization.
XgeneR can be installed in R with the following command:
devtools::install_github("pachterlab/XgeneR")