A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

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Documentation for package ‘trackViewer’ version 1.45.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

trackViewer-package	Minimal designed plotting tool for genomic data
$-method	Class '"trackStyle"'
$<--method	Class '"trackStyle"'
addArrowMark	Add arrow mark to the figure at a given position
addGuideLine	Add guide lines to the tracks
addInteractionAnnotation	Add annotation markers to the figure at a given position
ARA	Aggregate Region Analysis
browseTracks	browse tracks
browseTracks-shiny	Shiny bindings for browseTracks
browseTracksOutput	Shiny bindings for browseTracks
coverageGR	calculate coverage
dandelion.plot	dandelion.plots
geneModelFromTxdb	Prepare gene model from an object of TxDb
geneTrack	track from TxDb
getCurTrackViewport	Get current track viewport
getGeneIDsFromTxDb	get gene ids by genomic location
getLocation	get genomic location by gene symbol
gi2track	convert GInteractions to track object
gieStain	color sheme for the schema for Chromosome Band (Ideogram)
GIoperator	GInteractions operator
gridPlot	plot GRanges metadata
GRoperator	GRanges operator
ideogramPlot	plot ideogram with data
importBam	Reading data from a BAM file
importData	Reading data from a BED or WIG file to RleList
importGInteractions	Reading data from a ginteractions, hic, cool, or validPairs file
importScore	Reading data from a BED or WIG file
importScSeqScore	plot tracks for single cell RNAseq
listChromosomes	List the available chromosome
listNormalizations	List the available normalizations
listResolutions	List the available resolutions
loadIdeogram	load ideogram from UCSC
lolliplot	Lolliplots
optimizeStyle	Optimize the style of plot
parse2GRanges	parse text into GRanges
parseWIG	convert WIG format track to BED format track
plotGRanges	plot GRanges data
plotIdeo	plot ideogram
plotOneIdeo	plot ideogram with data for one chromosome
pos	Class '"pos"'
pos-class	Class '"pos"'
reduce,GInteractions	Reduce method for 'GInteractions'
reduce-method	Reduce method for 'GInteractions'
renderbrowseTracks	Shiny bindings for browseTracks
seqlevels-method	Class '"trackStyle"'
seqlevelsStyle-method	Class '"trackStyle"'
seqlevelsStyle<--method	List of tracks
seqlevelsStyle<--method	Class '"trackStyle"'
setTrackStyleParam	Class '"trackStyle"'
setTrackStyleParam-method	Class '"trackStyle"'
setTrackViewerStyleParam	Class '"trackViewerStyle"'
setTrackViewerStyleParam-method	Class '"trackViewerStyle"'
setTrackXscaleParam	Class '"trackStyle"'
setTrackXscaleParam-method	Class '"trackStyle"'
setTrackYaxisParam	Class '"trackStyle"'
setTrackYaxisParam-method	Class '"trackStyle"'
show-method	Class '"trackStyle"'
track	Class '"trackStyle"'
track-class	Class '"trackStyle"'
trackList	List of tracks
trackList-class	List of tracks
trackStyle	Class '"trackStyle"'
trackStyle-class	Class '"trackStyle"'
trackViewer	Minimal designed plotting tool for genomic data
trackViewerStyle	Class '"trackViewerStyle"'
trackViewerStyle-class	Class '"trackViewerStyle"'
viewGene	plot tracks based on gene name
viewTracks	plot the tracks
xscale	Class '"xscale"'
xscale-class	Class '"xscale"'
yaxisStyle	Class '"yaxisStyle"'
yaxisStyle-class	Class '"yaxisStyle"'