recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options.

recoup can be used for the creation of:

  • Average signal coverage plots which can be faceted according to several factors, including the provision of a design file, k-means clustering, sample-wise or a combination of these.
  • Signal heatmap plots, over genomic regions of interest, with subclustering and faceting over several factors.
  • Signal correlation plots, useful for checking whether total genome profiles for some biological factor/condition correlate with each other.