recoup

recoup calculates and visualizes signal profiles from short sequence reads generated by Next Generation Sequencing (NGS) to support analysis of ChIP-Seq and RNA-Seq experiments.

Key Features:

• Signal Profile Calculation: recoup summarizes sequencing read data into curve profiles or heatmap profiles to represent aggregated and detailed signal distributions.
• Visualization Libraries: recoup generates plots using ggplot2 and ComplexHeatmap within the R programming environment.
• Genomic Data Support: recoup is tailored for generating genomic profile plots from ChIP-Seq and RNA-Seq datasets.

Scientific Applications:

• ChIP-Seq Analysis: Visualize protein–DNA interaction profiles to aid identification of regulatory elements.
• RNA-Seq Data Interpretation: Examine gene expression profiles across conditions or tissues to inform transcriptional regulation analyses.

Methodology:

recoup operates within the Bioconductor framework using the R programming language, computes signal profiles from sequencing reads as curve or heatmap representations, and leverages ggplot2 and ComplexHeatmap for visualization.