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Fig. 2 | BMC Bioinformatics

Fig. 2

From: RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data

Fig. 2

Overview of RGT core classes and tools. RGT provides three core classes to handle the genomic regions and signals. Each genomic region is represented by GenomicRegion class and multiple regions are represented by GenomicRegionSet class. The genomic signals are represented CoverageSet class. These classes serve as the core data structures of RGT for handling genomic regions and signals. Based on these classes, we developed several tools for analyzing regulatory genomics data as represented by different colors, namely, HINT for footprinting analysis of ATAC/DNase-seq data; RGT-viz for finding associations between chromatin experiments; TDF for DNA/RNA triplex domain finder; THOR for differential peak calling of ChIP-seq data; Motif analysis for transcription factor binding sites matching and enrichment

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