Sushi: Tools for visualizing genomics data

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Sushi")
AuthorDouglas H Phanstiel <dphansti@stanford.edu>
Bioconductor views DataRepresentation Genetics HiC Infrastructure Sequencing Visualization
Date of publicationNone
MaintainerDouglas H Phanstiel <dphansti@stanford.edu>
LicenseGPL (>= 2)
Version1.12.0

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

Functions

addlegend Man page
chromOffsets Man page
convertstrandinfo Man page
labelgenome Man page
labelplot Man page
maptocolors Man page
maptolwd Man page
opaque Man page
plotBed Man page
plotBedgraph Man page
plotBedpe Man page
plotGenes Man page
plotHic Man page
plotManhattan Man page
sortChrom Man page
Sushi_5C.bedpe Man page
Sushi_ChIAPET_pol2.bedpe Man page
Sushi_ChIPExo_CTCF.bedgraph Man page
Sushi_ChIPSeq_CTCF.bedgraph Man page
Sushi_ChIPSeq_pol2.bed Man page
Sushi_ChIPSeq_pol2.bedgraph Man page
Sushi_ChIPSeq_severalfactors.bed Man page
SushiColors Man page
Sushi_DNaseI.bedgraph Man page
Sushi_genes.bed Man page
Sushi_GWAS.bed Man page
Sushi_hg18_genome Man page
Sushi_HiC.matrix Man page
Sushi_RNASeq_K562.bedgraph Man page
Sushi_transcripts.bed Man page
zoombox Man page
zoomsregion Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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