Sushi.R is written exclusively in the R software environment. The Sushi.R package includes 13 example datasets and a vignette detailing the usage of each (Sanyal et al., 2012 (link); Li et al., 2012 (link); ENCODE Project Consortium et al., 2012 (link); Neph et al., 2012 (link); International Consortium for Blood Pressure Genome-Wide Association Studies et al., 2011 (link); Dixon et al., 2012 (link); Rhee and Pugh, 2011 (link)). Datasets that were mapped to hg19 were converted to hg18 using the liftOver tool. Sushi is compatible with all organisms and genome builds. Large datasets were filtered to include only regions shown in Figure 1. ChIA-PET interactions were additionally filtered to remove interactions between regions ≤1000 bp apart. To facilitate use, Sushi.R is open source and is distributed through both Bioconductor for one-step installation and GitHub for version control, issue management and third-party development (Gentleman et al., 2004 (link)).

Multi-panel Sushi plot made without modification by external image-editing software. The Sushi functions used to create the plot include (A) plotManhattan, (B) plotHic, (C) plotBedpe, (D) plotBedpe, (E) plotBedgraph, (F) plotBedgraph, (G) plotBed, (H) plotManhattan, (I) plotBed, (J) plotGenes, (K) plotBed, (L) plotBedgraph, (M) plotBedgraph and (N) plotGenes. The code and data to make this figure are included as part of the Sushi.R package

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