Sushi: Tools for visualizing genomics data

Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures

Author
Douglas H Phanstiel <dphansti@stanford.edu>
Date of publication
None
Maintainer
Douglas H Phanstiel <dphansti@stanford.edu>
License
GPL (>= 2)
Version
1.12.0

View on Bioconductor

Man pages

addlegend
adds a legend to a Sushi plot
chromOffsets
defines chromosome offsets for plotting multi chromosomal...
convertstrandinfo
Converts strand info to 1 / -1
labelgenome
Adds genome coordinates to the x-axis of a Sushi plot
labelplot
adds a letter and a title to a plot
maptocolors
maps numeric vector to color palette
maptolwd
maps numeric vector to line widths
opaque
makes colors transparent (or opaque)
plotBed
plots data stored in bed file format
plotBedgraph
plots data stored in bed file format
plotBedpe
plots data stored in bed file format
plotGenes
plots gene structure or transcript structures
plotHic
plots HiC interactio matrix
plotManhattan
plots a Manhattan plot
sortChrom
sort chromosome files by chom name
Sushi_5C.bedpe
Sushi_5C.bedpe
Sushi_ChIAPET_pol2.bedpe
Sushi_ChIAPET_pol2.bedpe
Sushi_ChIPExo_CTCF.bedgraph
Sushi_ChIPExo_CTCF.bedgraph
Sushi_ChIPSeq_CTCF.bedgraph
Sushi_ChIPSeq_CTCF.bedgraph
Sushi_ChIPSeq_pol2.bed
Sushi_ChIPSeq_pol2.bed
Sushi_ChIPSeq_pol2.bedgraph
Sushi_ChIPSeq_pol2.bedgraph
Sushi_ChIPSeq_severalfactors.bed
Sushi_ChIPSeq_severalfactors.bed
SushiColors
Generates a Sushi color palette
Sushi_DNaseI.bedgraph
Sushi_DNaseI.bedgraph
Sushi_genes.bed
Sushi_genes.bed
Sushi_GWAS.bed
Sushi_GWAS.bed
Sushi_hg18_genome
Sushi_hg18_genome
Sushi_HiC.matrix
Sushi_HiC.matrix
Sushi_RNASeq_K562.bedgraph
Sushi_RNASeq_K562.bedgraph
Sushi_transcripts.bed
Sushi_transcripts.bed
zoombox
Adds a zoom box to a plot
zoomsregion
Adds a zoom region to a plot

Files in this package

Sushi/DESCRIPTION
Sushi/NAMESPACE
Sushi/NEWS
Sushi/R
Sushi/R/Sushi-internal.R
Sushi/R/SushiColors.R
Sushi/R/addlegend.R
Sushi/R/chromOffsets.R
Sushi/R/convertstrandinfo.R
Sushi/R/datasetsinfo.R
Sushi/R/labelgenome.R
Sushi/R/labelplot.R
Sushi/R/maptocolors.R
Sushi/R/maptolwd.R
Sushi/R/opaque.R
Sushi/R/plotBed.R
Sushi/R/plotBedgraph.R
Sushi/R/plotBedpe.R
Sushi/R/plotGenes.R
Sushi/R/plotHic.R
Sushi/R/plotManhattan.R
Sushi/R/sortChrom.R
Sushi/R/zoombox.R
Sushi/R/zoomsregion.R
Sushi/README.md
Sushi/build
Sushi/build/vignette.rds
Sushi/data
Sushi/data/Sushi_5C.bedpe.rda
Sushi/data/Sushi_ChIAPET_pol2.bedpe.rda
Sushi/data/Sushi_ChIPExo_CTCF.bedgraph.rda
Sushi/data/Sushi_ChIPSeq_CTCF.bedgraph.rda
Sushi/data/Sushi_ChIPSeq_pol2.bed.rda
Sushi/data/Sushi_ChIPSeq_pol2.bedgraph.rda
Sushi/data/Sushi_ChIPSeq_severalfactors.bed.rda
Sushi/data/Sushi_DNaseI.bedgraph.rda
Sushi/data/Sushi_GWAS.bed.rda
Sushi/data/Sushi_HiC.matrix.rda
Sushi/data/Sushi_RNASeq_K562.bedgraph.rda
Sushi/data/Sushi_genes.bed.rda
Sushi/data/Sushi_hg18_genome.rda
Sushi/data/Sushi_transcripts.bed.rda
Sushi/data/datalist
Sushi/inst
Sushi/inst/doc
Sushi/inst/doc/Sushi.R
Sushi/inst/doc/Sushi.Rnw
Sushi/inst/doc/Sushi.pdf
Sushi/man
Sushi/man/SushiColors.Rd
Sushi/man/Sushi_5C.bedpe.Rd
Sushi/man/Sushi_ChIAPET_pol2.bedpe.Rd
Sushi/man/Sushi_ChIPExo_CTCF.bedgraph.Rd
Sushi/man/Sushi_ChIPSeq_CTCF.bedgraph.Rd
Sushi/man/Sushi_ChIPSeq_pol2.bed.Rd
Sushi/man/Sushi_ChIPSeq_pol2.bedgraph.Rd
Sushi/man/Sushi_ChIPSeq_severalfactors.bed.Rd
Sushi/man/Sushi_DNaseI.bedgraph.Rd
Sushi/man/Sushi_GWAS.bed.Rd
Sushi/man/Sushi_HiC.matrix.Rd
Sushi/man/Sushi_RNASeq_K562.bedgraph.Rd
Sushi/man/Sushi_genes.bed.Rd
Sushi/man/Sushi_hg18_genome.Rd
Sushi/man/Sushi_transcripts.bed.Rd
Sushi/man/addlegend.Rd
Sushi/man/chromOffsets.Rd
Sushi/man/convertstrandinfo.Rd
Sushi/man/labelgenome.Rd
Sushi/man/labelplot.Rd
Sushi/man/maptocolors.Rd
Sushi/man/maptolwd.Rd
Sushi/man/opaque.Rd
Sushi/man/plotBed.Rd
Sushi/man/plotBedgraph.Rd
Sushi/man/plotBedpe.Rd
Sushi/man/plotGenes.Rd
Sushi/man/plotHic.Rd
Sushi/man/plotManhattan.Rd
Sushi/man/sortChrom.Rd
Sushi/man/zoombox.Rd
Sushi/man/zoomsregion.Rd
Sushi/vignettes
Sushi/vignettes/Figure_1.pdf
Sushi/vignettes/PaperFigure.R
Sushi/vignettes/Sushi.Rnw