├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── Sushi-internal.R ├── Sushi.R ├── SushiColors.R ├── addlegend.R ├── chromOffsets.R ├── convertstrandinfo.R ├── datasetsinfo.R ├── highlighthic.R ├── labelgenome.R ├── labelplot.R ├── maptocolors.R ├── maptolwd.R ├── opaque.R ├── plotBed.R ├── plotBedgraph.R ├── plotBedpe.R ├── plotGenes.R ├── plotHic.R ├── plotHic2.R ├── plotManhattan.R ├── sortChrom.R ├── zoombox.R ├── zoomsregion.R └── zzz.R ├── README.md ├── Sushi.Rproj ├── data ├── Sushi_5C.bedpe.rda ├── Sushi_ChIAPET_pol2.bedpe.rda ├── Sushi_ChIPExo_CTCF.bedgraph.rda ├── Sushi_ChIPSeq_CTCF.bedgraph.rda ├── Sushi_ChIPSeq_pol2.bed.rda ├── Sushi_ChIPSeq_pol2.bedgraph.rda ├── Sushi_ChIPSeq_severalfactors.bed.rda ├── Sushi_DNaseI.bedgraph.rda ├── Sushi_GWAS.bed.rda ├── Sushi_HiC.matrix.rda ├── Sushi_RNASeq_K562.bedgraph.rda ├── Sushi_genes.bed.rda ├── Sushi_hg18_genome.rda └── Sushi_transcripts.bed.rda ├── man ├── Sushi-package.Rd ├── SushiColors.Rd ├── Sushi_5C.bedpe.Rd ├── Sushi_ChIAPET_pol2.bedpe.Rd ├── Sushi_ChIPExo_CTCF.bedgraph.Rd ├── Sushi_ChIPSeq_CTCF.bedgraph.Rd ├── Sushi_ChIPSeq_pol2.bed.Rd ├── Sushi_ChIPSeq_pol2.bedgraph.Rd ├── Sushi_ChIPSeq_severalfactors.bed.Rd ├── Sushi_DNaseI.bedgraph.Rd ├── Sushi_GWAS.bed.Rd ├── Sushi_HiC.matrix.Rd ├── Sushi_RNASeq_K562.bedgraph.Rd ├── Sushi_genes.bed.Rd ├── Sushi_hg18_genome.Rd ├── Sushi_transcripts.bed.Rd ├── addlegend.Rd ├── chromOffsets.Rd ├── convertstrandinfo.Rd ├── highlighthic.Rd ├── labelgenome.Rd ├── labelplot.Rd ├── maptocolors.Rd ├── maptolwd.Rd ├── opaque.Rd ├── plotBed.Rd ├── plotBedgraph.Rd ├── plotBedpe.Rd ├── plotGenes.Rd ├── plotHic.Rd ├── plotHic2.Rd ├── plotManhattan.Rd ├── sortChrom.Rd ├── zoombox.Rd └── zoomsregion.Rd └── vignettes ├── Figure_1.pdf ├── PaperFigure.R ├── Sushi.Rnw ├── Sushi.bib └── Sushi.pdf /.Rbuildignore: -------------------------------------------------------------------------------- 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