Sushi: Tools for visualizing genomics data
Version 1.14.0

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

Browse man pages Browse package API and functions Browse package files

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)
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Sushi")

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

SushiColors Man page Source code
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
Sushi_DNaseI.bedgraph Man page
Sushi_GWAS.bed Man page
Sushi_HiC.matrix Man page
Sushi_RNASeq_K562.bedgraph Man page
Sushi_genes.bed Man page
Sushi_hg18_genome Man page
Sushi_transcripts.bed Man page
addlegend Man page Source code
chromOffsets Man page Source code
convertstrandinfo Man page Source code
labelgenome Man page Source code
labelplot Man page Source code
maptocolors Man page Source code
maptolwd Man page Source code
opaque Man page Source code
plotBed Man page Source code
plotBedgraph Man page Source code
plotBedpe Man page Source code
plotGenes Man page Source code
plotHic Man page Source code
plotManhattan Man page Source code
sortChrom Man page Source code
zoombox Man page Source code
zoomsregion Man page Source code

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
Sushi documentation built on May 20, 2017, 10:04 p.m.