ASEP, overcomes three analytical challenges, utilizes cross-subject and cross-SNP information to detect gene-level ASE under one condition and differential ASE between two conditions (e.g., pre- versus post-treatment) in a population using RNA sequencing (RNA-seq) data.

Please cite the following publication:

ASEP: gene-based detection of allele-specific expression across individuals in a population by RNA sequencing
J. Fan, J. Hu, C. Xue, H. Zhang, k. Susztak, M. Reilly, R. Xiao, M. Li
PLOS Genetics 16(5): e1008786. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008786

# install devtools if necessary
if (!"devtools" %in% rownames(installed.packages())) {
  install.packages('devtools')
}
# install the ASEP package
if (!"ASEP" %in% rownames(installed.packages())) {
  devtools::install_github('Jiaxin-Fan/ASEP')
}
# load
library(ASEP)

Please see Tutorial.