ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data

Summary In this article we present ChIPdig, a tool for analyzing and comparing multiple ChIP-seq data sets. ChIPdig is written in R and enables access to powerful R-based functions and packages through a simple user interface powered by the shiny package. It allows users to align reads to a reference genome, perform peak calling and differential enrichment analysis on regions of interest, annotate such regions based on available coordinates of transcription start and termination sites, exons, introns, 5’ UTRs and 3’ UTRs, and generate heatmaps and metaplots for visualizing coverage. Availability and implementation ChIPdig is open source and available at https://github.com/rmesse/ChIPdig. Contact rmesse@bu.edu or agrishok@bu.edu

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