Sushi: Tools for visualizing genomics data

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

AuthorDouglas H Phanstiel <dphansti@stanford.edu>
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

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

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