primaryAnnotation R package
This package was developed for two purposes: (1) to generate data-driven transcript annotations based on nascent transcript sequencing data, and (2) to annotate de novo identified transcriptional units (e.g., genes and enhancers) based on existing annotations such as those from (1). The code for this package was employed in analyses underlying our manuscript in preparation: Transcriptional mechanisms and gene regulatory networks underlying early adipogenesis (this note will be updated upon publication).
See the vignette and user manual:
Warren Anderson, Mete Civelek, Michael Guertin