DENR

Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) performs annotation based transcript level quantification on nascent RNA sequencing data. Although it was developed on PRO-seq data it should be generally applicable to any nascent sequencing dataset which has been processed such that each read is represented as a single count representing the 3' end of the transcript being synthesized. For a pipeline to process PRO-seq data in this manner see the Danko Lab's PRO-seq 2.0 pipeline here. DENR quantifies nascent transcript abundance based on reference. Package can be installed with the following line of code:.