Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
30 September 2025
Analyzing paired count data using edgeR
Lizhong ChenWEHI Bioinformatics
edgeR is an R package for analyzing sequence read count data from genomic sequencing technologies such as RNA-seq, ChIP-seq and ATAC-seq, using negative binomial generalized linear models. We usually analyse only one count matrix, but another dataset with a paired counts becomes popular, like methylation data using BS-seq and recent F1-hybrids allelic data. edgeR does provide an option to analyse such data using a paired design appoach but it has many limitations. In this talk, I will introduce a new quasi-likelihood method using quasi-binomial model for the paired count data. It starts with a PCList object and follows the same edgeR QL pipeline. It is computationally faster and has more power compared with existing methods. Last, this technique can be applied to cell composition and differential usage analysis beside edgeR