derfinder

derfinder is a software tool to address the limitations of current differential expression analysis methods for RNA-sequencing (RNA-seq) data. As RNA-seq technology becomes more cost-effective and replaces microarrays for genome-wide expression measurement, there's a growing need for analysis methods to discover differential expression beyond the confines of known genes without the complications associated with transcript assembly and abundance estimation.

derfinder introduces a novel approach by first assessing differential expression at each base across the genome, identifying differentially expressed regions (DERs) of interest. It then segments the genome into regions where bases exhibit similar differential expression signals, assigning statistical significance to each segment. This base-level analysis allows for the discovery of differential expression in areas outside previously annotated genes, offering a significant advantage over traditional methods limited to known gene boundaries.